A note can be many things depending on the actual key the song you want to play is in. It could be the root, or a third or tritonus etc. Interval names are completely independent from any key and could therefore be used universally. When I think of harmonies I think of intervals first.
I believe you would be in the minority with it working for you easily.
Are you able to look at the Eventide GUI as a point of reference?
(I could send you screen shots of a H8000 re it's custom scales GUI & it would add context to my comments & request if you like?)
At the end of the day it's all chromatics regarding notes & there are no 100% rules/formulas regarding their use creating unique harmony.
You could choose the key which of course would be the root note as a point of reference for the custom scales however, any & all notes thereafter could/would be chromatics as far as the KPA is concerned and you would select any note to match/offset the one the KPA detected 'you' playing into it.
Note names are the best & truest way to make custom scales in the most easiest, fastest & logical fashion unbridling any rules/formulas on the player.