The motor mount alignment tool helps to keep the motor from being mis-aligned. If the motor is aligned correctly to start with, and if you only remove one mount at a time, you shouldn't have a major problem with alignment issues. If you have removed all four mounts at once, as when the motor is removed and replaced, the alignment tool is really helpful. It is used in place of the mount at the front of the engine, beneath the radiator, to insure a proper alignment of the other three mounts.
I know in my Mustang it really doesnt matter. 
