Okay, I know this is probably ridiculously over-simplistic, but from a conceptual stand-point, how about something like this?
From the user side, you would simply select LaTeX as your export method. I do not see why you would need any other checkboxes or drop downs (except maybe the localisation bit), or the confusion of selecting Plain Text first. While technically everything will be handled as plain text, the user only cares about what comes out at the end, be that a web page, a LaTeX book, or an RTF.
A warning would come up (with a NeverShowAgainFlag) informing the user that all RTF formatting will be lost, and that documents without MMD syntax will be converted to plain text. Presumably, if a person were formatting their Draft with MMD for the purpose of eventual LaTeX export, they probably will not have very many RTFs hanging around, anyway.
With the LaTeX exporter, having an MMD flag at all seems redundant, since everything is getting converted to plain text. But of course, it is necessary for the other exports, where the MMD document would get converted into an RTF first, and then added to the working stream.
I think, this would mean there would be two different pre-processors. The LaTeX pre-processor would convert Scrivener annotations and footnotes into MMD analogues, so that they are properly converted into LaTeX. But the RTF/XHTML/PlainText exporters would want to retain the Scrivener mark-up, so that they get properly handled by Scrivener, not MMD. MMD flattens footnotes.
Actually, does that mean the MMD=>XHTML script would never be needed? If everything gets converted to RTF internally, and then Scrivener does what it does from that point on – I think not? Although, on the other hand, I would miss the ultra-clean XHTML that it generates, as opposed to Apple’s nightmare version of it. 
Annotation and Footnotes Syntax Example
This would only need to be done for the LaTeX exporter. Footnotes are the easiest, just convert Scrivener footnotes into this:
[code]Here is the text stream[^1], and so forth.
[^1]: And here is the referenced text.[/code]
The next would be [^2] and so on.
Annotations are a something to think about. It might be nice to actually convert them into LaTeX’s version of a comment. But this would require an extra few steps, because you cannot insert raw LaTeX into an MMD file, it will try to be smart and escape all of the characters that make it work. So, you would want to create some sort of unambiguous start and stop in the pre-processor step, say:
[A[Here is the text of the annotation.]A]
And then, after the LaTeX file has been completely generated, go through and replace all of those so that the final result looks like:
\marginpar{Here is the text of the annotation.}
This will set the annotation into the margin area of the page, and of course if the user is versed in LaTeX and wished it to look some other way, it would be a simple matter of overriding the appearance of the marginpar environment, or changing it entirely with search and replace. Whether or not this method is used could even be tied to the current “Export annotations as RTF comments” option. Just change the label to “…as LaTeX comments…” when relevant.
The only major problem I see is that doing it this way would lose the positional context of the annotation. I think in Word, doesn’t it place a little icon where the comment is in the text, or does it remove it from the context as well? Some consideration could be given to this, if you wanted context retained – I know I would.
The other option is to simply format them into the text the way RTFD does and whatnot. Either way, adding colour might be nice. That would look like:
\marginpar{\color[rgb]{1.0, 0.0, 0.0}{Here is the text of the annotation.}}
If you wanted to do that, you would need to add this line manually to the final LaTeX output:
\usepackage{color}
If you open up a generated LaTeX file, you’ll see a section near the top that has a block of these \usepackage declarations. It can be added anywhere in this top part of the document. To make it easier for you, you could just have it insert on line 2 or something.
So, if the user has the annotations as comments thing un-checked (or if you decide against using marginpar), the code would be:
\color[rgb]{1.0, 0.0, 0.0}{[Here is the text of the annotation.]}
