Ash, the onus is on them to prove a modification you have made caused and problems.
They still have to cover you for anything that's not your fault. So really there's not much point in waiting until it's out of warranty.. as if it's the modification that's going to break the car, you'll be paying for it whether it's in warranty or not.
So go right ahead get your 300bhp from a simple exhaust and intercooler change. (Can you detect the jealousy in that statement? )
EDIT: as an example, if you fit an intercooler... and a month later the water pump started leaking, they'd have a hard time proving that one lead to the other. In fact, they couldn't, because it didn't.