I looked onto this a few years back when mine was still in warranty and was advised by a bloke from Seat UK that the responsibility is on the dealer to prove that the change made has directly caused the failure being claimed for and that only parts directly affectedy can be deemed excluded from warranty (I was asking about a theoretical remap - that I'd already had done!). So in your case, if your gearbox fell off, you would be OK. If your MAF failed and it was oiled up from the filter oil then you'd be paying for both parts and labour for the new MAF.
It doesn't stop a dealer simply saying "no" and making it your
problem, but in those cases go to a different dealer, name and shame them on here and give them no further business as they are not discharging their responsibility as a main agent.