I does work that way....
You just have to always program the 'Global Custom Scale' while temporarily transposing the scale to the key of 'A', And with the Pitch block temporarily set to the 'key' of 'A'. So that the note names will match whatever you are playing. Play an 'A', adjust the 'A'... Play a 'C', adjust the 'C'. etc....... All the while, adjusting the 'Shift Intervals' for each note while still temporarily playing the notes of scale in the 'key' of 'A'.
Once you have done this... That custom scale can be used in all keys simply by selecting that custom scale number and the 'key' in the 'Custom Shifter' type in the 'Pitch' block.
You just have to always program the 'Global Custom Scale' while temporarily transposing the scale to the key of 'A', And with the Pitch block temporarily set to the 'key' of 'A'. So that the note names will match whatever you are playing. Play an 'A', adjust the 'A'... Play a 'C', adjust the 'C'. etc....... All the while, adjusting the 'Shift Intervals' for each note while still temporarily playing the notes of scale in the 'key' of 'A'.
Once you have done this... That custom scale can be used in all keys simply by selecting that custom scale number and the 'key' in the 'Custom Shifter' type in the 'Pitch' block.