I think they'd be nuts to extend a warranty to a modded light. They generally have no control over it, and no idea how close to the edge of failure the modder goes.
However, there is a precedent for approved "mods" in some products. For example, you can buy a Leupold rifle scope, have a particular company (Premier Reticles?) change the reticle and/or the magnification, and it will still be under warranty. This is a pre-arranged deal with Leupold though. They will not extend warranties to cover every modder.
PS: The thing is, say the modder accidentally overstressed the lens, or put a chip in the edge. Then maybe through normal use (bumps, thermal stress, etc.) the lens cracks. At this point, through no fault of their own, and despite their best preventative efforts, Surefire pays for parts and labor to fix the light. The end result is that I pay more for my next Surefire to cover those kinds of costs. The modder should be the one to offer a warranty on the light after the mod.