Just dont cut it so short that it limits your options on down the road. With tackle, batts, gas tank, fishermen in the back of the boat, make sure you still have enough shaft to go into the waves up front in case you decide to longline out the back or something. It doesnt hurt for the tm to stick up when in use as long as the tm fits inside the gunnell of the boat when stowed.
That's true. I removed a 42" motorguide and installed a 48" powerdrive with an i-pilot. Just adjust the shaft length to your needs. Still fits inside the boat while stowed - didn't want to cut.