Just to sum up what I have learned in the meantime: It is not possible for the kind of book I wrote to do a print and an ePub-eBook version with the same document. Reason being is that the print version (and an PDF Version viewed on an iPad or similar device) uses tables and a range of colors that look stunning on a medium to large display (and hopefully also in print, will take a while), but the hardware of ePub devices is too limited to achieve it there.
It's like the old days with Netscape, Explorer, and Oracle -- only worse. Tables look awful unless you format them manually (InDesign does not export them with formatting), and using a colored table-style does not make sense on a small device (screen too small for the tables to look good with this kind of margin effect and some device offer no color, i.e., the information value vanishes).
So the best solution is to create an own ePub version -- removing any color, replacing the tables (and the need for a color scheme) with bullet point lists, and keeping to basic formatting. But doing both with one file is -- I think -- not possible for the formatting I have used, it would only cripple the print version/PDF ebook version.
Another problem is the formatting of the InDesign file itself -- there is a great guide to use InDesign for ePub creation here (unfortunately in German), e.g., the text has to be on continuous flow (it was not).
So, I think the answer is -- there is no need for such a color scheme if ePub is included, because you can never be sure that the reader is using a device that can display any color. If going for print/PDF ebook and ePub, with complex formatting you might have to create two versions of it.
@Moderator: Not sure, should I have written this as an addendum to my question? Or not at all?