Lists tend to give a more dispassionate sense, and so may be less appropriate in fiction. Your example might be rephrased as something like:
His flower-patterned shirt brightened his otherwise drab knit cap and faded jeans.
His knit cap and faded jeans denied the spring cheer declared by his flower-patterned shirt.
or even a more neutral
He was wearing faded jeans topped with a flower-patterned shirt and knit cap.
In this case, using a list with a preceding categorization might be appropriate:
He was dressed casually—faded jeans, a knit cap and a flower-patterned shirt.
As you noted, there are tradeoffs between logical ordering and lyrical ordering. Comprehensibility and contextual significance add further tradeoffs.
a knit cap, a flower-patterned shirt, and faded jeans
is a logical ordering—top to bottom. Logical ordering can be usefully mnemonic, especially for longer lists. As they introduce an expectation, starting with a logical ordering can be used to increase emphasis on a contrasting element. E.g.:
faded jeans, a flower-patterned shirt, a knit cap, and bunny slippers
This gives a sense of the viewer's gaze moving upward and then going back to the feet with less emphasis than taking the last item out of the list like:
faded jeans, a flower-patterned shirt, and a knit cap—and bunny slippers
Alphabetical or acrostic ordering is less likely in fiction, but more common logical ordering would be by typical significance such as rarity (including rank, cost, or even peculiarity), by location (e.g., progressing vertically, horizontally, along a meridian, along a parallel), and by time. A strong logical ordering implies a significance to the ordering principle.
E.g., when listing places to which a character has traveled, time ordering gives a biographical feeling and may be important to placing events described later or reveal aspects of the character's personality. A geographical ordering could emphasis a logical migration or flight (even if the path in time was not so regular) or a logical homing on a critical location. Ordering by population/urbanization or tourist popularity might present a feeling of logical character development. Declining popularity or population might subtly imply increased isolation, self-confidence (not relying on social support structures), or eclectic tastes; increasing on that scale might imply increasing conformity, self-acceptance (not being burdened by social disapproval), or sophistication.
These effects can—and often should—be subtle and, if intentional, their effects may need to be reinforced by further context. E.g., in the example list, the downward movement of the gaze might very weakly imply an initial looking at the face with some emphasis on social interaction but then a downward examining of social signals (perhaps implying a lack of familiarity or even a judgmental attitude). This might be used to reinforce a perception of social disapproval given by other cues. An upward movement might imply that the viewer initial looks more downward which might imply social awkwardness, possibly general, sexual, or related to social standing. This might be used, e.g., to emphasize the excellence of the character or to encourage a sympathy with a character's social awkwardness.
If the reader identifies with the narrator (as if mentally describing the scene), subtle cues can place the reader in relationship to the character or setting by declaring how the reader sees the character or setting.
The lyrical aspect of ordering is probably more important than logical ordering for short lists. Ordering can influence the position of stressed syllables and the strength of alliteration and assonance which can influence the pacing and atmosphere of the text as well as the emphasis of items (countering or reinforcing the position in the list). Avoiding or exploiting alliteration or a particular meter may justify using a non-logical ordering.
He was wearing faded jeans, a flower-patterned shirt, and a knit cap.
might be slightly more appropriate in a more upbeat setting because of the mild alliteration and the ending of the list and sentence with a pair of stressed syllables. Whereas
He was wearing a knit cap, a flower-patterned shirt, and faded jeans
minimizes alliteration and moves the paired stressed syllables to the beginning of the list where the emphasis is somewhat muted by being in the middle of the sentence. This ordering might be more appropriate for a more somber mood. Conceptually, ending with "faded jeans" would also fit a more somber mood and placing "flower" in the middle reduces its upbeat sense. Moving "patterned" closer to the end and to "faded jeans" may also very weakly imply a dark fate, but that is likely an imagined impression.
Like the lyrical aspect, the length and conceptual complexity of items may be significant in choosing the ordering most appropriate for the sense being communicated. Long or conceptually complex (or even unfamiliar) items are usually less disruptive at the beginning or end of a list because they slow the reader.
For unfamiliar items, placement at the end of a list allows later explanation without a distant antecedent, though a very brief explanation of the first item may also avoid reader disruption since the list has not yet been observed as a list.
For a long list, such a slowing of the reader may be used break the list into two parts, which may make such a long list more readable without violating the perception that it is a single list (e.g., consider the pause effect of "five gold rings" in "The Twelve Days of Christmas").
Contextual significance of the items is another consideration for ordering. A list ordered by common significance gives no additional contextual information beyond the scale and direction chosen. If the items have substantially expected ordering, then any exception is likely to feel jarring (which may be the desired effect) or emphasize items placed out of expected order. A ham and cheese sandwich is ordinary, a cheese and ham sandwich emphasizes the cheese.
If the items do not have a strongly expected order, then the order can be used to more subtly communicate impressions specific to a setting, scene, or characters. The readers generally expect an ordering to have meaning even if not significant meaning, and the writer can exploit this non-conscious pattern recognition to effect implicit observations. Affirming and subverting such implicit observations have well-known effects, but neglecting them can also be useful to allow different audiences to understand the work in different ways (the "let the reader imagine" alternative to "show" or "tell") or to encourage a curiosity about whether the observations are correct.
As has been mentioned, subverting such guidelines can be used in much the same way as other forms of subverting the reader's expectations. Subversion can include using a different scale or direction than seems obvious from the items with the revelation near the end of the list or only later in the story. Even the use of a list can imply some significance which expectation can be affirmed or subverted. E.g., in a mystery,
the drawer opened smoothly to reveal a stash of stationery and pens, a silver letter opener, and a small jar of rubber cement
might deceptively emphasize the items in or absent from the drawer when the significant clue is in the drawer opening smoothly.
Finally, consider the following:
The felt-lined interior held only four items: the key to his first car, his mother's wedding ring, an individually-wrapped Tootsie Roll, and a picture of June.
The first two are obviously items of sentimental value and the list seems to be progressing in intensity of sentiment, though a historical progression would also make sense. The picture is understandably the most significant (or most recent), but the positioning of the candy in such a list in anomalous. Placing this anomaly next to the most significant item intensifies the mystery; the proximity to the picture of a presumed lost love and enclosure between two romantic items might hint at the candy being significant to his relationship with June. This ordering also makes the picture more ambiguous; there is an alteration between positive and mixed feelings—a presumably positive (unless the car is associated with a painful memory) feeling, mixed grief and love, comfort, and whatever the picture represents.
If the candy had been placed first, a historical order might be reasonably assumed: childhood, late adolescence/early adulthood, his mother's later life and death, and finally June. In which case one can almost imagine the character asking himself "Why did my summer come so late?".
An ordering of key, candy, ring, picture would de-emphasize the candy and bind the ring and picture more closely together. An ordering of ring, key, candy, picture might be taken as reversed historical order, implying that June was significant in his early childhood and remained significant. An ordering of ring, key, picture, candy might imply an order of descending significance, making the picture more mysterious since one is less likely to keep a picture less significant than that key in a special collection; the candy as least important would also be less strange.
This list is naturally more emotionally charged than a list of clothing someone is wearing, but subtle cues in ordinary descriptions can be used to enhance the presentation.
For lists generated by characters, the character's nature and circumstances should usually be more important than effects like mood setting, but this does not exclude using ordering for external effect, especially when the character's choice would otherwise be arbitrary.
As with any writing, what is being communicated should guide choices and not all decisions are equally significant.