Firstly, what version of Scrivener and MMD are you using?
You shouldn’t be seeing any code, but I can’t really offer any advice until I know what system setup you have.
Not in that particular fashion. As documented, the RTF output is meant for quick proofs and such where it does not matter much what the document looks like, or even if it has proper footnotes, figures at all, etc. It depends on what version of MMD you have—for a bit there an experimental XSLT was used, but before and after that, RTF is produced via the UNIX utility, textutil, which just took the XHTML file and did a straight formatting conversion to RTF.
If you want a full-blown word processor output file, use Flat ODT. You might need to upgrade to MMD3 for that; or just download the Scrivener beta, which inclues MMD3.5 (or 3.6) and fully supports the new system.
With .fodt, you should use Nisus Writer Pro or LibreOffice to open the document and from there you can convert it to whatever word processing format you need. That will be fully featured with stylesheets from the top down, proper cross-references, etc.