Absolutely yes. The problem is they are accessing and modifying something that they do not legally own (IANAL --- but the terminology they use when referring to paying and then being able to use a vehicle they made sounds very much not a rental or a lease), regardless of what that modification is.
To stretch the analogy, I would be just as pissed if GM decided to send someone to my house and replace the tires on my car with new ones, and I couldn't do anything to stop them.
Furthermore, the whole VW emissions thing shows what real ownership means --- they came up with an update to reduce emissions (and likely power or fuel economy...), and probably very strongly encouraged owners to get it, but ultimately if someone bought the car then they can't just go and "fix" it, even if they were found to be violating emissions laws, because they still need consent from the owner.