If you cut the fork tubes down, then the fork tubes are effectively "riding higher" in the triple tree. For example, if you cut two inches off the tubes then you have effectively raised them 2" in the trees. This does nothing to reduce the amount of travel, so when these "raised" fork tubes "bottom out", they are also bottoming out 2" higher than before. Will this cause the fender to hit the lower tree?
The spacers on the piston work great for me, although my efforts were to lower and stiffen the front for drag racing. I used a 1-1/2" long 3/4" I.D. 1" O.D. brass bushings for spacers on the piston. I did not cut the springs either so the front of my bike now sits 1-1/2" lower, and the springs have an 1-1/2" of preload. This is the same as ratchet strapping the front suspension down 1-1/2" and the upper limit of travel remains in the same place as before. I can always remove the bushings to revert the forks back to stock length. EZPZ.
No brainer for me. Good thing too...