Thanks so much! I also had a lot of problems when starting. There were more than a few cases where I was trying to use a single tool with mediocre results for the sake of using a single system instead of matching the task with an appropriate tool and accepting a little bit of a extra work (when the payoff wasn’t yet apparent).
I’ve been hoping GoodNotes to release a URL scheme to directly open a note in the native interface, similar to how Obsidian and some others have URL schemes to open specific objects directly. I’ll definitely look into your suggestion on using the automatic PDF backups as the entry point, particularly when I just need to reference something quickly.