If your only going to be keeping the car for a couple of years, then maybe it's not worth voiding the warranty. If something serious goes wrong with no coverage, you'll put money into repairs that will be washed out by the KBB value. For example, the value of two similar '04 GSR's that have had their transfer cases replaced are going to cost the same. The only differance is that one was covered under warranty (no cost) and the other was paid out of the owners pocket (money lost). Does it make sense?
For me, I'm in for the long haul so I'm not conserned about the warranty and I'm modding away.
I'll probably have this car for 10 years and if anything goes wrong, it's getting upgraded; bottom end, tranny, transfer case, whatever. I'll get my money's worth out of the parts and labor because I'm keeping it so long.
I hope this makes sense and helps you.