In mathematics, computer science, physics, or economics, a publisher might want to work from your files, which they will assume you have written from scratch. And they may expect to be able to swap in their house class or style file to achieve the look they want. A PreTeXt file will look a bit unusual, see Section 30.17. On 2022-11-22 we have a report of a very extensive research article 1  written in PreTeXt and uploaded to the arXiv 2  preprint server, where it was successfully processed by pdflatex on the server, with only minimal hand-edits to the intermediate file. We can always improve in this area, so we welcome reports, good and bad, about the robustness of our output when delivered to publishers.
arxiv.org/abs/2211.11671
arxiv.org/