Part of the problem goes back to some of what I way saying about, about how internal links tend to point to headers within a single document, so their usage intent doesn’t really overlap with [some text](binder%20title.md). I.e. I suppose we could make a checkbox that does that, it probably wouldn’t even be that difficult, but ordinarily you wouldn’t be using links for that purpose, and rather something more like, “See Subsection 12.8.3 (pg. 172)” in the final output.
But speaking of multi-file output scripts, you may have come across it before, I made a simple demonstration of using compiler post-processing, with a simple Ruby script, to generate a folder of .md files. Or really, it could be other types too, as demonstrated earlier in that thread, where the script runs MMD on each split-off file to generate a folder of .tex files.
Not too far away from what you made, it sounds like, though maybe the idea of coupling an automatically executed script with a compile format that inserts file markers is new. It makes it the sort of thing you can do one day, and then switch to another Format and get a singular .tex file the next day.