Drivetrain 2003 pilot bearing

It seems to me that the lip on the pilot bearing only controls the depth of the bearing into the crank shaft. The transmission input shaft is supported by the inner diameter of the pilot bearing.

The only way I see this causing a problem is IF the new bearing's lip is soooooooo thick it prevents the input shaft from going in all the way. But you stated that the new bearing's lip is actually thinner.

OBTW. Most of the pilot bearings I have installed have no lip at all. Just a straight piece of metal.