Apple will not be making any product changes to Catalina in 2021, and there is no knowledge that Apple fixed anything related to that previous post, or your current experience in Big Sur either. Manually poking around in a PDF is not recommended, as that document format is not linearly organized, one can destroy the PDF, and most have not memorized the PDF specification to know what they are doing. That said…
I have never experienced vanishing annotations that I have created in Preview, on any prior or current release of macOS. I have created annotations in other PDF readers that Preview would not show, and yes, those annotations were still in the PDF corpus, and were revealed again in the originating PDF reader when reopened. As much as we would like, there is no universal annotation implementation. If there is any question, I fall back on the current Adobe Acrobat Reader DC as it is the standard reader that Adobe keeps current.
The annotations in Preview are listed by its Inspector's (⌘i) Annotations Inspector tab as shown here.

It would show notes, and other annotations, but I have not included them because it uses the actual username, instead of the anonymouns name set in Preview Preferences > PDF panel.
My recommendation is to do all of your future annotation and PDF reading in Adobe Acrobat Reader DC, which eliminates issues with Preview annotations. Do not mix PDF viewers and annotation creation sources.