Strange indeed, I played around a bit further and the only thing I could come up with was this combination of features:
- In Section Layout, under the “Title Appearance” tab, check off Insert title as run-in head.
- In the “Title Prefix and Suffix” tab, add two carriage returns to the Suffix to essentially undoing the above.
Who knows, maybe that was it, or maybe some other odd combination is lurking in there.
Scrivener will, yes, but that is not the same as saying MultiMarkdown will. The content will still matter, as Scrivener won’t insert around the document in order to signal to MMD that this section of text should be handled verbatim. What this flag does is opt that document out of what the Formatting pane does. With that pane you can even have some items not export their text, or add things like document notes. A document flagged As-Is would just print the text from the editor no matter what, no added title, no added meta-data—and with rich-text folk, it also means the body text will remain formatted as they set it up in the editor, too, rather than having the compiler normalise the formatting. It’s a way of breaking out of the strict outline-based style system for exceptions—like a bunch of short sections that should read as one unbroken string of paragraphs. Maybe you as a writer want more outline than the reader will need, that sort of thing.
If that’s what you’re looking to do, then the regular old plain-text option in Scrivener may be the best approach. You do miss out on a few things, because that truly is plain-text—no footnote feature, no inline images, etc. I mean you can use the things, they just won’t export as LaTeX syntax—it doesn’t know anything about that and can only generate .tex files thanks to MMD.
That aside, you do still get a lot of potential convenience. You’ve already been exploring the Formatting pane’s prefix and suffix features, with plain-text you don’t have to work around hashes, you have a clean slate. A simple example, you can set level 2 files to have the following:
Prefix:
\section{
Suffix:
}
\label{<$title_no_spaces>}
The code in angular brackets is a Scrivener code that will insert the title of the document without spaces. Now if you compile a file with the name, “Installing Ruby Gems”, the compiler will print:
\section{Installing Ruby Gems}
\label{InstallingRubyGems}
Thus you could map your binder outline to ToC entries in the final output, among other things. Replacements of course provide a lot of flexibility, especially once you dig into the more advanced uses of it. For example here’s an easy way to get around the lack of a footnote export with plain-text. Of course one can just type in \footnote{too}. 
I’m an MMD-head though, so I am inclined toward shortening syntax and processing short form to long form in one sweep.