If your crank is not drilled and you use a bearing that goes in the outer register cutting the excess off the end of the input shaft that would normally go into the pilot hole of the crank will have no impact on input bearing life nor will it damage the tranny. The input shaft will be supported by the pilot bushing closer to the splines than with a conventional bushing.
Also, if you have an unfinished pilot hole that is not to full depth and use the thin wall bushing trimming the end of the input shaft that extends beyond the bushing to prevent it from bottoming out will not shorten the input bearing life nor will it damage the tranny.
The only reason not to do it is that it prevents the tranny from being used with a conventional pilot bushing in the future.