Yeah I think overall the rule of thumb is that the beta is good enough for daily work now, but compiling is still under construction, so you can’t expect that to be working right yet.
At the moment it looks like I can remove the Title and Author default fields from my project, but they pop right back up after I compile, so I have to remove them every time. However so long as I do remove them, I get a “snippet” style .tex file with no other support files in the compile folder (oddly enough, as I was getting a different result yesterday, I’ll have to look into that one a little closer).
And in case it wasn’t clear from my earlier description, the Format is not where this kind of metadata is typically specified, and certainly not by default. Any metadata going into a Format ought to be the sort that would be applicable to a dozen different projects. It’s an export template, if you will, not this project’s settings. So that is all the last place you would want to put something so very specific as a working title.
Yes, I write the user manuals and will be working to get this whole area up to spec during the beta. But as for what you can do, there is a beta forum that the is actively monitored and maintained. Don’t worry about the issues I’m bringing to light here in this discussion, I’ll investigate & report them.
Speaking of the user manual, you might want to grab a copy of the user manual project itself. It’s not going to help you much on the compile side of things, but you might be interested to see how a PDF like the ones you can download from the page for the Mac, is put together on the Scrivener side of things. The most important thing I see missing at the moment is the Section Layout prefix and suffix tabs, where some of what I do to compile this project will be missing.
Lastly, I wanted to return to your original post:
Do you mean to say that up until now you’ve been basically compiling using the MultiMarkdown engine, but then wrapping your entire text in an HTML comment so that MMD does nothing? That you are basically writing your own LaTeX syntax directly into the editor in all cases?
If so, why even use MultiMarkdown? 
The only thing that’s giving you is conversion from Markdown syntax to LaTeX syntax, which you aren’t using from the sound of it.
Well you might like our LaTeX template once we get that finished. It was designed specifically for people that do not want to learn Markdown or deal with any conversion engines, and want to simply compose in LaTeX, using Scrivener like a fancy tex editor basically. The compiler isn’t ready for this template, so there is no sense in trying it, but I figured that might be something you would want to keep in mind for the future.