I don’t see the contradiction.
Substrate is the thing it’s made out of. It’s more typically discussed with computers: computation has the same rules whether you build a computer out of silicon or any other materials.
Deutsch is saying that epistemology would work the same for AGIs even though they are made of different materials than humans are made of. He also believes that different AGI designs won’t change epistemology, similar to how different (classical, non-quantum) computer designs are unable to change what algorithms a computer can run (unless you handicap the computer – you can get it to run less but not more).