There's absolutely no problem with cutting the knob side of the shifter short to shorten the throws. It actually does reduce the throw length of the shifter.
It does, however, move the shifter further from the steering wheel and closer to the center armrest, which can bother some folks. It forces you to use a non-OEM shifter, which could bother some folks. And it doesn't get you the same precision feeling of lengthening the rod side of the lever. There is also a counterweight added to the short shifter, which helps to reduce the notchiness in the shorter shifts.
I use a Momo short anatomic shifter on my Rx-7, which shortened the shift throw somewhat and really feels nice, but in the case of the Boxster, I like the position and design of the shifter as it is and decided this route, which I am very happy with.
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