LaTeX absolutely sucks for proofing. Typos end up being buried in tags, and you end up with a document that looks pretty but possibly not fully edited.
If you are collaborating with advisors, they may wish to add comments to your copy as you work through your thesis. There is no clean way to do this in a TeX source file, so the only way to do this would be to export your work-in-progress into a DOCX, and then work your changes back into your source.
Versioning-by-hand sucks balls. When you’re approaching various deadlines with other obligations at hand, all open-source kumbaya ideas go out the window and you just make do.
For your manuscript_final_FINAL_v2.docx file, manual layout tuning ends up being not too bad and likely takes less time than troubleshooting LaTeX which might not have as much documentation.