Actually, if you're in the US the Magnuson-Moss Warranty Act covers you in the case of customizations [1]. Under this law, manufacturers are only able to claim your warranty as void if the modifications are what caused your warranty claim. I doubt they would be able to claim that your custom ROM caused your hardware failure on the USB port, so legally they had to fix it. More info on this FTC law [2].
I'm in Europe, but it may well be that a similar law is in effect here. However, a lot of consumers (me included) wouldn't know about that, and companies try to get out of repairs that they are legally required to perform.
Take a look at Apple's warranty: they claim to provide only 1 year of warranty, while European law requires them to provide two years. They will repair your device in the second year (it's the law!). However, I bet their confusing labeling etc. will cause a lot of people to believe their warranty has expired. Those people will either not ask for a free repair or pay their shop to repair the device.
In the US, Magnuson-Moss is often referred to as "the lemon law" (a defective product that can't be repaired is colloquially called a "lemon"). Specifically, "the lemon law" refers commonly to cars that have issues the dealer didn't specify before the sale and will not/can not fix.
Problem is, the FTC requires you to have a lawyer file a lawsuit and coordinate your legal costs and representation with the FTC, generally requiring a lawyer specifically dealing in lemon law cases. I've been down this path with a defective cell phone (HTC Touch Pro) and trying to get my carrier to replace it, and it's impossible to find a lemon law lawyer that deals in anything besides used car sales.
As always, the law is well intentioned but enforcement is next to impossible, just like you said.
Take a look at Apple's warranty: they claim to provide only 1 year of warranty, while European law requires them to provide two years. They will repair your device in the second year (it's the law!). However, I bet their confusing labeling etc. will cause a lot of people to believe their warranty has expired. Those people will either not ask for a free repair or pay their shop to repair the device.