Why go that way? Why not just go straight from Markdown to ePub? We even have a pretty well automated setup for it in the compiler, if you have Pandoc installed. You can set up the cover, ToC settings, stylesheet, etc. It’s a very good quality ePub too, in my opinion.
That aside, no Scrivener doesn’t really have anything like this. It can fake it with tab stops and bookmark cross-reference links, but that’s mostly just for quick and dirty proofing. It’s not dynamic based on the content. This post describes the preferred way of doing this, which on the Scrivener side is less about the ToC and more about getting the document properly structured, so that it can be easily added post-compile.
Back to Markdown, if you use the Pandoc → DOCX output, you’ll find a ToC tab. That will insert the codes, and with the document styled properly already, probably work just like you want out of the box.
As for the formatting of it, itself, well that’s what stylesheet and template documents are for. Manually going in and creating the formatting you want by hand every single time is something we should never have to do, even if you aren’t using Markdown to generate documents.