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.

My recommendations are Firefox, Okular, Inkscape and Draw, depending on usecase.

Firefox is perfect for text-based markup (so higlighting, defacing with text, etc.)

Okular is a bit worse on the text front (doesn't support editing the markup - for most stuff your only option is to undo so you have to be strategic abput catching mistakes early), but it does more stuff (boxes, arrows, lines, transparency, custom colors).

Draw is better if you actually want to make changes to many pages at once and don't care if it messes up formatting a bit.

Inkscape is ideal if you want to rearrange stuff on a few pages and change things like colors or stamp on some text. It doesn't have a nice way for highlighting text, but highlighting stuff like drawings, etc. is easier (just draw a recrangle with 30% opacity). Unlike Okular, changes aren't baked in and unlike Draw, it's easier to play around with colors and opacity.