Hi there, on KSP user scale you can remove all notes: there is no concept of root note.
You just set the notes you wish to have in your scale (from 1 note to 12 chromatic notes).
It is because the scale quantization doesn't take in account the harmonic role of the note within the scale.
If you have a G major scale and change it to a A major scale, the G notes in your sequence will be transformed into G# (and not A) because it will quantize the note to the closest lower note.
To breifly summarize the user scale is just a choice of note but does note take in account Root note and/or intervals.
In your case the C major pentatonic = D minor pentatonic if that makes sense
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It would be such an awesome feature tho! Next level scale quantization !
I hope it helps!