I opened bitcoin core with no wallet.dat, so it generated a new, empty one, with no bitcoin or transactions.
How exactly did you do this? Did you shutdown Bitcoin Core,
move (not copy) the original wallet.dat file, and then start Bitcoin Core?
Does bitcoin core store the private keys somewhere other than wallet.dat, or when a new wallet.dat is created on the same computer, is it deterministically linked to previous wallet.dat's created on that computer?
No.
In short, how did my existing wallet.dat get the private key I imported when running a different, brand new, never before used wallet.dat?
It would appear that you've either imported that private key before... or you hadn't actually opened Bitcoin Core with a "new" wallet.dat and you imported it into your "original" wallet.dat