This sort of issue has already been tested in court and, at least here in Europe, generally seems to follow common sense. For example, if a new top-of-the-range smartphone suffers a hardware failure after 3 months, the manufacturer can't disclaim any responsibility for that and exempt themselves from our normal consumer protection standards just because the owner had flashed custom firmware onto their device (unless the custom firmware was actually a causal factor in the failure, presumably, though I'm not sure that scenario has been tested in court yet).

Right, and unlike a lot of other cases with software, how this was decided might actually result in jail time. For example if a modification was deemed negligent and resulted in the death of a person, whoever made/authorized the modifications could be charged with manslaughter/murder.