I don't think shortshifters has anything to do with first gear synchros. It doesn't matter if you took that plate off or modified it because it's YOUR car. The dealer cannot deny the warranty service (notice, it's not voiding) on the first gear synchro just because they saw chopped off plate near the shifter.
You can do whatever to your car as you please, but IF the aftermarket parts you installed or any modification caused the system to fail, you have to be responsible for the consequence.
I don't think short shifter alone will cause any problem in the car.
P.S. BTW, if your friend forcefully shifted into first a lot, the synchro prolly got beaten to death. He wouldn't be able to push into first above 5mph(some say 10mph) without double clutching. That's normal.