IME, the difference in scale is (playing fretted) not noticeable in the fingers. It does something with the shoulder and neck, though, which is not nice at all!
Playing fretless, there may be some, eh, variation in intonation when one is really trained into one scale length and change into another scale all over sudden and for a short time.
However, if one practice with all available scale leghths, the change becomes no prob!
So, I switch between 750mm (30"), 34", 874mm (34.4") and 41" URB, and the variation in intonation is there for less than a minute, when switching. And I'm not even well practiced right now!