I'm at the other side of the note system trade-off thingy. I use Apple Notes.
It's not perfect, but if I really want better search functionality, I'll just use the SQLite database that stores the notes. I've never needed to roll up my sleeves for that. I get around the limitations.
It's not perfect, but crafting one's own Personal Knowledge Management System sounds like a 5 year journey for 10 to 20 hours per week at least.