Liability is the least important part of this problem. It doesn't matter who is liable, the problem is a conflict of philosophies. On one side we want to ensure the safety of the public, on the other we want to have full control over the equipment we own.

This isn't the first time this question has come up. It comes up with firearms for example, regarding how you can and cannot modify on a firearm you legally purchased.

IMO you should be able to modify your car's autopilot however you want to... at the expense of being able to legally drive it on roads. We already have fairly strict legal requirements in place for you to be able to take a 2+ ton death machine on wheels and travel in it at high speeds on public roads.

And also whether the modification is relevant the the problem. I can imagine court cases where the driver argues that the change they made was irrelevant to the accident that occurred.

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.