The SOA warranty is unaffected
This is just plain BS. Read your warranty booklet.
If by some chance the engine or tranny grenades, SOA won't pay as the engine is modded (unless the dealer lies to them - I wouldn't want to rely on that). You can bet the dealer won't pay for it out of their own pockets.
Does Cobb's warranty cover their components or the entire drivetrain?
If it only covers their components (which it sounds like), ask yourself this question:
Do I have $3-4k cash in the bank to pay for a new engine if I blow this one up?