Were that me (I used KP), it would be in a different kdbx file. This is one of the benefits of KP, I have about 8 different vaults for various things. I don't like putting my eggs in one basket.
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.
The URL field in KeePass has lots of convenient features [0], but unfortunately they're quite "obscure" and not very discoverable.