If your concern is about the lack of a clear migration path, Obsidian vaults are just folders with markdown files, which can be used with absolutely anything, you can literally use them in Emacs or VSCode if you want. The most popular PDF annotation plugin is AGPL-3 licensed and its format is also transparent so you can migrate to something else.
Not really, markdown has tons of tiny implementation details. And I can not use PDF annotation plugin in Emacs...
> markdown has tons of tiny implementation details. And I can not use PDF annotation plugin in Emacs
The same can be said about any other open format, I guess. There's no free lunch, you're always locked in by the implementation/workflow details, and have to write actual code (or use the code written by someone else) to migrate off to a different tool. The point is to not be locked by the format obfuscation or the storage.
I need to be absolutely sure PDF annotation tool will be around in a year 2050! Obsidian may withdraw their subscription offer at any time! Or raise subscription to $10000 per year (someone here says much higher price would be a steal!). I will always be able to run Logseq PDF annotator! Maybe in virtual machine. Or I will patch it (I have source code!!!). I have control over it!
And I really really hate fiddling with plugins. I was never much of Vim/Emacs guy for this reasons (prefer integrated IDEs such Idea). Logseq just works without setting up dozens of plugins and scripts. I use vanilla version with two plugins (video timestamp annotations and extra theme).