I'm posting this as a separate Topic as it separately applies to two different mods I tested, and I don't want to copy-paste the same issue twice when it may have the same root cause.
The Issue: When Loading a Stock Craft into a KSP Game with EITHER Waterfall or Realplume loaded, Engine Enable/Disable Action Groups get lost.
How it should be: how it ends up with either RealPlume or Waterfall:
Probable Cause (guess)
The issue does not appear to lie in the configs directly,