"This is a pretty unique edge case. "
I happen to work on a user manual with about 150+ Rmd files, 200,000 words, hundreds of images/screen captures... So I kind of jumped directly into the deep end of the bookdown pool
"Can I break a chapter onto multiple Rmd files and merge the whole thing?"
I meant can I create a bookdown with multiples Rmd which are either chapter and subsections. So the answer provided by @dapeng is right and allows the structure you referenced (with each row being a Rmd and a gitbook html):
Ch 1a: intro part 1
Ch 1b: intro part2
Ch 2: some stuff
Ch 3a: long chapter part a
Ch 3b: long chapter part b
Ch 3c: long chapter part c
Overall, I would say that it is a matter of adapting the solution to the specific content and need of the book.