I think you are right -- if the frame split or broke near the rear pin, or in some way a fault could be traced to the modification of the beavertail, the warranty would definitely be voided. And the frame is the gun, and is expensive.
Having some confidence in S&W customer service, however, I don't think they would void the warranty as it affects some other part of the pistol because of a modification that is not related to the specific failure. Not unlike the situation with installing an Apex kit. They don't warranty the Apex part, obviously, but they cover the rest of the pistol.
Now, why remove the beavertail? Because of the ancient urge to put one's own mark on a possession -- to customize the weapon a little bit. And, based on the compacts, I think the M&P looks better without it. Clearly, it is not required if the compacts don't have it. It is one of the modifications that Mr. Burwell has performed on M&Ps shown on his web site. With it gone, the M&P full size becomes a little shorter and easier to handle. But it is pure personal preference; I don't recommend it for anyone but me!