the above posts mostly ring true from my experience.
I will add that most dealers say that any mods they both sell and install will not void your warranty in any way. (which doesn't make ANY sense from a logical perspective but is an awesome "business decision" from a profitability standpoint).
Big 4 seemed to be in the know about the laws regarding the subject at least, in that they understood that the law says the mod needs to have caused more than 50% of the problem to jeopardize warranty.
Tower made statements of their policy that blatantly contradicted law, such as "If you install a snorkel, we will assume you've been mudding and all coverage will be denied" (straight from the keyboard of their service manager, Baron Ellis).
In the end I decided to just get a 2 " lift, a winch, bumpers, etc first, and worry about the more serious mods after the warranty is over.