In both cases I have some concern about privacy. For the search, a malevolent app may search for "e" or " " and get all the user notes without express consent. Same things can be done for common tags like "bank", "family" or "work". The risk is compromising user's security. Am I too concern?
On Macs, on the other hand, any apps can have full r/w access to Bear database.sqlite, so not much difference.
Not sandboxed apps (the ones on the Mac App Store).
The token is indeed a very brilliant solution (no wonder it comes from Ulysses), maybe can be generated in-app by a preference functionality and pasted by the user who wants to access to security-critical xcallbacks.
I'll keep it in mind if more people request this kind of functionalities.