What would the bill be for? "Changing stuff you own"? When did we wholly give ourselves up to the idea that the manufacturer owns the stuff we bought, and they can penalize us for messing with their things?
They will see malware in the ECU. If a system is compromised by "obvious malware", other systems could be also. If there is a possible danger for your physical integrity any sensible worker will worry and take actions, specially before it evolves into a legal danger for them.
They will not hesitate to change the Electronic Control module and maybe the BSI also, just to be sure that your car don't fails in the worse moment and kills you. This could start at 1500 euro or much more depending on the brand. They will not understand your "right" to run Doom in your car.
Think also that currently some secondary car systems in many brands can be deactivated online, without creating a situation of danger for you, but making your driving experience really miserable if they want.
If you modify your car with an aftermarket part, and take it to the shop, they aren't going to yank out your aftermarket parts because they're "worried about liability." They're going to leave it there, because it's your car, not theirs. It's not their job to stupid-proof your vehicle, it's their job to fix it.
They will bill for the time lost chasing md5sums at least. You need to understand that cars are a bunch of computers now; but a laptop is not expected to kill you, and a car will. The risks associated with messing with the car are much higher.
And if you think that, lets say "BMW", will hesitate a second to block online your car heating in the middle of winter; think again. I had seen it before. Even if you could hack it, to reconfigure the system again is not always easy or obvious without some knowledge of what values you need to enter.
You're confusing how things are with how they should be, though. I'm legally liable for any modifications I made to the car, so the manufacturer or repair garage should leave my property well alone.
It's not up to the car's maker to in any way interfere with or dictate the way I use my car.
They will not hesitate to change the Electronic Control module and maybe the BSI also, just to be sure that your car don't fails in the worse moment and kills you. This could start at 1500 euro or much more depending on the brand. They will not understand your "right" to run Doom in your car.
Think also that currently some secondary car systems in many brands can be deactivated online, without creating a situation of danger for you, but making your driving experience really miserable if they want.