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I recently wrote my Bachelor's thesis (±19.000 words) in LaTeX using Git, and it worked wonderfully! My project structure wasn't as complicated as what you're planning on though – it was simply a .tex file, a .bib file and I gitignored almost everything else (images, PDF's, etc.). /u/milou345's suggestion to use TeX.gitignore is definitely a good one. I made sure to have a backup for all the non-text files, of course.
If you want to take some inspiration I used this template for my master thesis, which does everything I described above.
For example code of this and automated upload to s3 see: https://github.com/robert-will-brown/cv