I'm pretty convinced even as early as the late 17th century the 2 main versions of the ballad had different tunes. Bronson would verify but even today the overwhelming selection of tunes gives us the 2 main tunes for most versions. With such a widespread ballad it would be astounding if there wasn't a wide variety of tunes as well. We also need to take into account that from early stages long before the tunes were being recorded the ballad was available with sheet music in both main versions. The 'Scotch' version tune is much more arty and that is one of the reasons I think this is most likely the version that Pepys heard being sung by Mrs Knipp in the 1660s.