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Xournal++ is my go to. It has a few quirks to get used to, but once you do it's quite functional. Biggest thing to watch out for is exporting and overwriting the source file. It will usually let you, but it often blanks out the source and loses your changes. So just make sure to export with a different filename than the original is. If you accept the default suggestion, it will work fine.

It's also made to be used well with wacom tablets, so if you have one of those you can make use of it in xournal++.

The older "Xournal" (no ++) is mostly functional but also dead, so I would go with Xournal++.

PDF was not created to be edited, but as a final output format ready to be printed as-is. OTOH, XournalPP has basic editing tools. So does LibreOffice.

I can't answer windows/linux, but I use pdfexpert.com for mac and it's great. It was a one time $100 charge when I bought it several years ago, and it gets updated regularly.

Thanks, but I'm more likely to use Windows or even TempleOS over MacOS.

Have a look at Qoppa, Master Pdf Editor, and Xournal.