It seems obvious that Aunt Molly Jackson's "Archie D." is one of her ballad recreations, not a text learned from tradition. But how can it be that her and Joe Rae's tunes for this ballad are so similar?

To make matters more complicated the 2nd half of Nic Jones' folk revival tune for "Annachie Gordon" also resembles both tunes unless my ears are failing me. The "Buchan's bonny" part is different, but when Nic Jones sings "For Annachie Gordon, oh he’s bonny and he’s braw", that's similar.

The Liner Notes of Nic Jones' album "The Noah's Ark Trap" (1977) say:
For Annachie Gordon I adapted the tune found in Christie’s Traditional Ballad Airs and collated verses from Lord Saltoun & Auchanachie (Buchan’s Ballads of the North of Scotland), Young Annochie (Murison MS), and Lord Saltoun & Annachie (Christie’s Traditional Ballad Airs).

So the Child 239 tunes from Aunt Molly Jackson, Joe Rae and Christie’s Traditional Ballad Airs are all similar. I wish I had an explanation but this mystery might remain unsolved.