*shrug* Kinda sucks but I can understand why they do it. Doesn't bother me too much, I don't plan on sending my Bionic in even if something goes wrong. As a matter of fact I don't think I've ever sent any of my phones in for repairs, warranty issues, etc. Knock on would, I've never needed to.
It's only BS if they start refusing repairs that are clearly unrelated to you rooting or rom'ing your phone. If you send in a phone with a headphone jack that won't output any audio or a screen that it starting to warp, if they refuse to do anything just because you've triggered the root counter in recovery, that would be really lame. They're smart enough to know what rooting and rom'ing your phone can or cannot break.