I cannot imagine why they wouldn't void the warranty when the purchaser makes a material change to an important part of the saw. Especially if the warranty claim pertains to a part of the saw that is related to the modified muffler. For a broken throttle linkage or leaky gas cap or something like that, I doubt that the muffler would become an issue. But seriously, the saws themselves don't really cost that much in the first place, so what's the worst that happens - you have to pay a few bucks out of pocket for a repair?
If you're really concerned about warranty coverage, keep the saw bone stock.