I was possibly going to do a more robust EXE file... A commenter had some good ideas like BSA extraction/creation automation with BSA commander, which would help people with patching the vanilla BSAs, and I could verify checksums and what not even.
Of course, that all deals with just the vanilla meshes... Most PyFFI-ing doesn't take nearly as long, so what exactly is the need for patching in PyFFI? I'm not against it, just curious.

I could see it working in the In/Out environment. An additional Patches folder which generates the Patches after PyFFI has finished running (although the two-part INI process kind of mucks that up). The optimize-in-place PyFFI-ing seems more tricky. Of course the In/Out/Patches environment is identical to the way the patcher is currently set up, which is why it'd work well there.
Let me explain. PyFFI has an option to create patches directly (--diff), and also an option to update nifs using patch files (--patch) - actually this was supposed to address the issues with the original patcher batch files. But I never really documented it properly, and never included xdiff or similar. Also, it only uses in/out (confusingly) - an extra "patches" folder as you suggest, would be much better.
So I think I'll upgrade this feature to do essentially what your batch scripts are doing (but it wouldn't rely on forfiles.exe and so on).

Yes, will do!!
Aside, as it looks now, these updates won't be for 2.1.8, but more likely for 2.1.9, as I'm compelled to ship 2.1.8 already this weekend to release some longstanding bug fixes for the blender nif scripts, which require an updated pyffi.