Yes, it will probably mess up your engine centerline.  Also, remember that mounting ears are usually machined on one side to be parallel and flat for mounting.  The cast tops are not square, and you could risk distorting the case and ruining the engine.

I know on smaller engines, you could move the centerline up to 1/4" by mounting it on the "wrong" side of the ears.  If the ears are thicker on the gasser, and I'm assuming they are, it could put your centerline off even more.  So your cowl won't line up correctly( assuming enclosed engine), or even worse, could create an evil handling plane because the thrust line isn't correct.