I'm not really sure, but it may just be a matter of who you talk to whether you can get it swapped out or not. I was under the impression that Superior, Yukon, etc all covered flanges. After making some calls around, official word from all is that flanges are not covered.
I've seen guys wheeling hard enough to snap, sheer and warp some lesser made chromo shafts, but I've personally never seen a Nitro shaft with a broken shaft, warped splines or bent flange. However, like I said... their official position is it's not covered either. I'm curious now though if there's differences in materials and the process of making them between companies. Will report back with what I find out.
EDIT: Well, that was quick. Ten Factory covers flanges. Bend, break, whatever and they'll replace them.
Additionally, the process that is put into the shafts are also put into the flanges, so no difference in materials, however because of the way they are machined and treated, the treatment may not be consistent on the actual flange itself. Learn something new every day.