Typst for a PhD

That’s a personal preference. I did end up using tinymist, but it didn’t enforce that AFAIR.

I did write the whole document from the web app as I wanted my supervisors to be able to post comments (which is a feature that was released during my writing). I did the very last polishing steps within neovim (using tinymist).

For the bibliography, I aggressively split the .bib files across the file tree.
All my references were tracked within Zotero. To put it in Typst, I exported it to bibtex and copied that to my bib files in Typst. I know there’s a “Zotero sync” feature now, but I was probably fine with the manual workflow.