The alignment tool is for "fine tuning" the engine. The motor should, almost, fall right back into "good enough" alignment if the mounts and shims have not been altered while the motor was out. The pipe is solidly bolted to the motor at the exhaust manifold top and sides so the only way for the pipe and box to not line up is in the motor alignment.
The alignment tool should be able to slide into the pto flywheel with as little as possible contact or binding. It's not a "cram it in and call it good" tool. When I did the rebuild on my 94 xp this summer I replaced my home made shims with some real seadoo shims and spent 45 minutes adding, removing, lifting, lowering corners or the entire motor until I had the best alignment. During that whole process the tool slid into the flywheel easy, but you are looking for very slight changes of resistance and adjusting that out.