I've used xournalapp++ recently mostly to sketch diagrams as I would on paper. I don't see it as a real note taking, just paper replacement.

That said what you said is absolutely true and in my projects idea folder I called this "Inner knowing". The main problem is that note taking apps are marketed as a replacement for human memory ("brain dump", "second brain", etc). Hence they create a dependency on them as they decrease the ability to remember. When infact what we need is the opposite. Also I believe it should be an OS/DE feature thightly integrated with file management/search.

Yes, i've tried obsidian, it somewhat works but it's always an electron nonsense.