It's hard to get around this with the modern generation of powerful brakes with reasonably short throw - Formula / Trickstuff require similar so I wouldn't hold it against Hayes. Not perfect but better than the alternatives in my book. I've been replacing rotors more often to make sure they're true, the rub can cause forward pitching on larger jumps.Had to try 4 different 203mm rotors until I could find one that was straight enough to not rub from side to side on Hayes A4s, and that is after attempting to straighten while measureing with a dial indicator. They seem to need to be within 0.003". Great brakes but the required rotor tolerances are much tighter than even Hayes seems to produce.
I do think this is one area where TS offer some benefit over cheaper brakes though, the polished stainless slave pistons in anodized 7075-T6 bores seem to hold more consistent return distance over the life of the brake. The quality of this interface becomes more important when rotor clearance is reduced.