LibreOffice Draw can do markup and much more, the downside like OP mentioned is that sometimes the formatting of the PDF can get messed up so it’s a bit hit-or-miss.
Beyond that try Firefox (yes the web browser), its PDF markup capabilities are way better than you’d expect and the PDF formatting tends to stay intact. It’s probably better than LibreOffice for simple markup stuff, I just wish Firefox included a way to draw straight lines/arrows and shapes (circles, squares, etc.) to complete the markup toolbox. It does have a pen and highlighter but drawing an arrow via mouse looks a bit janky, LOL.
If you do a lot of the same type of markup (say an arrow pointed right) you could probably just save an image of an arrow and keep pasting it into the Firefox PDF editor, it’ll probably look better vs drawing them out.





That’s a pretty good one, hadn’t heard about it until you mentioned it. xournal++ is great at marking up PDF files and was able to keep the layout formatting intact with my janky test PDF (a sad document that must have been print-to-pdf’d multiple times under Windows).
I also like that it’s easy to use and has just about every markup tool you’d want, all the stuff that Firefox is missing.
Only thing missing is that it doesn’t have the advanced .pdf export options that the other tools have, but that’s kind of minor… figure I could open/re-export the marked up .pdf in another application if I really want to configure any advanced .pdf options for the final document.