I'm struggling to see the substantial difference between "self driving car with modified software should be disallowed because safety" and "manually driven car should be disallowed because safety".
The former is still strictly safer.
I find this to be an absolutely ridiculous statement. Software as we know it today is incredibly brittle. What will eventually be put on the road as fully autonomous vehicular control software will have been HEAVILY QA'ed, and will be continuously QAed by telemetry. Random people modifying that software invalidate any proof-of-safety from the upstream QA and monitoring processes.
You have drunk drivers, texting drivers, distracted drivers....
The human attention span is incredibly brittle as well.
In terms of QA'ing a manual driver in the US? You take a 10 minute driving test when you're 16 and you're licensed to drive for the rest of your life.
And I'm not saying your agency isn't worth other peoples' lives, but the argument that this doesn't matter because it would be rare is silly. It's still a decision that will have to be made and it's an interesting question nonetheless.