Ahh I didn't notice that the mutation also affects the ghosts' behavior. That does make sense! I agree, too, with your decision to make it invokable instead of automatic.
If you were going to make the player phase through boxes, you might just nudge them to the nearest free spot if they stop on a box when the mutation runs out. Would definitely require some checks, but it would seem natural to me.
(My comment about "wasting" the mutation was only my first thought, before I continued on, so it was eventually clear).
Kudos to Tunglith! Great job on the music, I'll have to see where I can give them a follow!