Not uncommon. Lots of boats have little grinder scars or cut structure where things are "clearanced". Really just fixing mfr's goofs.
If shaft run has only one cutless bearing and floating gland, engine can be lowered and aligned in that position. With two cutless bearings or a hard mounted gland, kinda SOL, and time to get the grinder.
Or a stiff leg can be put between stringer and deck and jack it up a touch.