I am not concerned with it. Some might be. My thought on this is, if I am not bypassing a rev limiter, or messing with air/fuel, I am not hurting it. I don't see where gears or a driveshaft would affect it, but thats just me.
Now if the rearend goes out, they may not fix it if you had gears installed. But, I certainly don't see how they could void the rest of the cars warranty.