That's true regarding the one file convenience but from another angle it's a separation of concerns, especially considering it's a pdf accessed very occasionally.

I maybe half agree with you about the encrypted overlay filesystem but only in respect to files, not passwords though. I tend not to keep files in KP, if I need a singular encrypted file I'd probably 7zip it (7z format) with a password and encrypt the filenames. The password goes in KP as does the location.