The PDF specification explicitly describes annotations and highlights, so any app that may learn PDFs ought to be capable to show them, and any app that saves PDFs ought to save them.
Apple’s PDFKit produces annotations and highlights which can be to spec, so they need to be suitable with different readers. I’d recommend it is a bug if they are not.
The one non-standard implementation that I do know of is that MacOS’s Preview makes use of proprietary Bookmarks, which can’t be learn by different non-Apple functions. Bookmarks from Acrobat and different PDF apps will seem within the Desk of Contents sidebar in Preview and different Apple PDFKit-based apps.
