Scientific journals do edit the TeX file. Both to update the visual style (e.g. enabling commercial fonts that they use for print but are not allowed to distrib

Scientific journals do edit the TeX file. Both to update the visual style (e.g. enabling commercial fonts that they use for print but are not allowed to distribute with the template), and to update the content itself (to revise the grammatical style to fit the style guide followed by that journal, to update scientific references to have clickable links, etc.). Usually, at the end of all these edits, the journal sends a PDF “proof” back to the authors to verify that the final version is OK, or ask for corrections if they broke something (which they often do).