From the Scrivener for Windows documentation (emphasis mine):
If you need your work to enter a standard word processor workflow, this will be your go-to method. MultiMarkdown's ODF support is comprehensive [... meaning the document can] use the table of contents feature of a word processor. It represents the only output method in Scrivener that offers this support, making MMD an enticing option for those who do not mind learning how to use it.
The documentation goes on to explain that LibreOffice (and OpenOffice, with the correct update installed) supports this format, and from there you can convert to other popular formats.
So (as I understand it) the process should be:
- Convert to OpenDocument Format, resulting in a
- Open in LibreOffice, and create table of contents.
- Export to format of your choosing.