I cannot use MMD because it’s not compatible with BibLaTex, so I have to resort to plain text. But the problem is that plain text does not allow me to compile the header, preamble, and footer. Should I use MMD LaTeX anyway and have Transformation change the Natbib footnote coding?
There isn’t anything in the Transformations compile pane for that, but did you ever get a chance to try the method I described before?
For now the link is too technical for me… Need more baby steps
All right, let me know what I can do to help then. 
On the original question, you might be making things more complicated than they need to be. If you are using Scrivener to produce LaTeX documents via its plain-text compile, then why not put the preamble, footer and other stuff into the Draft so that when you compile the result is a single, ready-to-typeset .tex file? You could even use the Front Matter feature for the preamble and such, keeping those files out of the Draft entirely, only inserted when you need them upon compile (you’ll still need the footer, but being at the bottom of the Draft that’s hardly in the way of anything).
Or you could just work the way MultiMarkdown does, with \inputs. Why not put your preamble and other .tex files into the folder you will be compiling to and typesetting from, and then refer to these files in your Draft with inputs? You don’t even need to put the .tex files into your compile folder if you have them in your texmf folder.
These options are easier, thanks!
I am using Option 1, putting my preamble and footer into the Drafts folder, but I am considering now using MMD, Option 2, and moving everything into the compile folder in Finder. Initial question is whether I can compile into a folder directly, without having Scrivener compile everything into a subfolder as it’s now doing
The compile folder concept and how MMD works with it is documented in §22.5.1 of the user manual, starting on page 335. It is possible to do what you are aiming for, I use that method myself for a number of projects which rely upon extensive external LaTeX resources that are not included in the compile output manifest.