Automatic array bounds checks can get hit by corrupted data. Thereby leading to a crash of exactly the kind that SQLite tries to avoid. With complete branch testing, they can guarantee that the test suite includes every kind of corruption that might hit an array bounds check, and guarantee that none of them panic. But if the compiler is inserting branches that are supposed to be inaccessible, you can't do complete branch testing. So now how do you know that you have tested every code branch that might be reached from corrupted data?
Furthermore those unused branches are there as footguns which are reachable with a cosmic ray bit flip, or a dodgy CPU. Which again undermines the principle of keeping running if at all possible.