MultiMarkdown generates HTML5 documents, which yes, are not compatible with ePub2 (you need XHTML). I would consider using Pandoc to generate your ePub, actually. If you set Scrivener to compile to basic MultiMarkdown instead of going straight to HTML, then with only a few tweaks, in most cases, you can then make use of Pandoc against that file to generate an ePub (either ePub2 or ePub3). It does a pretty decent job, and has a good level of customisation so you that you can streamline the process going forward—such as providing meta-data XML files, CSS, and even supporting most MMD conventions (like the MMD meta-data block).
Thanks for your answer.
Unless I’ve missed something, Pandoc seems to be a command-line tool only. So, I think I’ll stick to Sigil, that can do the job perfectly well, too. I’ll just have to do a couple of Search-Replace commands to get the markup I need before applying customized stylesheets, and produce the final epub.
If you want to see what you have to type on the command line to convert from text markdown to epub, this is the version that I have used successfully on Windows: