The scorcher is a fool-er. It is a plug and play harness under your engine cover. As far as I know, when the scorcher is removed there's no foot print like a tuner leaves.
A SCT tune or LMS tune reflashes the computer and leaves a foot print in the computer. A custom tune is a HUGE improvement over stock but warranty complications come into affect.
Whether or or not the fund will kid your warranty is the on going debate, but I can tell you that Ford will have final say in warranty claims. In order for something to void your warranty, Ford has to prove that aftermarket item caused a failure. In the case of a tune, nearly everything is affected. One way or another, Ford could say the tune changed this manufacturers setting, which caused this.