Say I go to an unauthorized service provider to get my car fixed. They swap out my engine with one that is so flaky and fragile that it explodes if you change the ignition timings.
Then I go to my original dealer and ask for them to update my software. The software update from my dealer changes the ignition timings because they've found more efficient timings.. The software update works fine with the original engine, but with the new engine it explodes.
Who's fault is it?
I'll give you a hint, at some point along the way you signed a piece of paper that says that the manufacturer only covers problems with their design or manufacturing.
Companies can't possibly be expected to test their software will all possible configurations of third-party modifications.