I'm kind of conflicted about needing to align the motor after a pull.
Many of the engine removal tutorials say to remove the entire motor mounts; however, the manual indicates that what aligns the engine & pump are actually the shims & motor mounts.
So if you can remove the top bolt instead of the entire motor mount and shims as many tuts say, in theory, your engine will be aligned using your pump and drive shaft.
The tool itself bolts onto the jetpump studs, and sends a rod through to the engine so it's centered. The engine itself should be balanced if it was built / rebuilt to spec.
In theory, you're doing the same thing If you leave the base of the mounts and shims, install the engine, align the PTO cover and front engine mount over the motor mounts so the top holes align, install the bolts for the motor mounts but leave loose so they're adjustable, install the drive shaft, bolt the pump on with the drive shaft installed.
In theory you're doing the same thing as the alignment tool.