Yes, their tool askes you to launch a CMD shell and type in a command via ADB to get your phone's unique code, so that you can copy and paste it into their website and then they email you the unlock code that is unique to that phone.
So they know that that particular phone has been unlocked, and you clicked that you agree that you are aware that you are voiding your warranty.
IMHO, I think it should only void the warranty if you brick it. If the screen cracks or a button falls off, it obviously has nothing to do with an unlocked bootloader.
Just voiding it entirely is like putting in an aftermarket set of speakers in your car. Maybe it voids the radio warranty because you could short something out, but if you throw a rod or the transmission falls out, it is clearly unrelated...