If you think about it for a minute, it makes sense. The gun manufacturers don't have any control over the quality, or lack thereof, of handloads.
Handloaders make mistakes. Sometimes those mistakes result in destroyed guns, and injured shooters or worse. There's another thread on the forum that talks about this.
With that in mind, I'd be surprised if there was gun maker that didn't put a stipulation in the warranty that the use of handloads would void any warranty in the event of a malfunction.
The most common malfunction over the years is feed jams when using wadcutters. The 1911 was designed to use hardball (230 g. FMJ) ammo, and will shoot them all day with no feed jams. Put a wadcutter in the mag, and you'll likely see more feed jams than smooth operation. Is the fault of the gun? No. So, why should the manufacturer pay for something that isn't their fault?
If you think about it, the same idea applies to cars with catalytic converters. There are little stickers all over the car that say "UNLEADED GAS ONLY," and for good reason.
Fill up with leaded gas, and you'll burn out the converter. Should the car manufacturer pay for a replacement if the car is still under warranty? No, because the owner did something that he was told not to do, and destroyed the converter in the process.