This means you cannot use Solomonoff induction to figure out the correct quantum physics, because Solomonoff induction works on the input stream of bits that it sees, not on the "universe as a whole".

This is a general problem: most decision theories ignore the fact that their implementation runs on physics, or make some nonsensical assumptions like "everything is program". But observations are not just parameters of a known idea (for agent's decisions, and in particular epistemic decisions, are not known), they by themselves mean at least the physical facts that constitute them.