I'm trying to figure it out with little luck as of yet unfortunately... when running setxkbmap using a different folder it's clear some default behaviours are being loaded from the normal xkb dir, such as altered ctrl functionality. I don't know how to use the command to load a completely new layout without it being coloured by the setup in the original xkb directory but will let you know if I figure it out.

Could you update this thread as this merge happens as this is a big issue for me?

Cheers mate