what would happen

You could. The reason to take it out is that the area that needs to be ground off is on the underside of the arm.
It may be possible to remove the arm from the mechanism by driving out the pin that holds it together, thus avoiding removing the whole shifter. The pin is inside the rubber boot. I would be afraid of bending the shaft by using a drift and hammer, but maybe a press type tool with a screw driven drift could do it. It is scary taking apart a chunk of your tranny, but it is not really difficult and if you are careful, there should be no problem putting it back together.
 
i'm not worried at all, just trying to save some steps. I'm done with performance for right now, going toward suspension and drive train.
 
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