"I am sympathetic about warranty anxiety, and history doesn't help; some dealers will let you get away with nearly anything, some will try and deny a claim if you have blacked out the bowtie, it seems completely arbitrary."
It really does come down to the dealer and how much they want to be jerks about it. If you do come up with a powertrain issue though, the first thing any dealer is probably going to want to do is reflash it to stock and drive it.