When I installed Signal recently I was asked for a passphrase. What is this passphrase used for if not to encrypt my messages?
However the page that you linked does not mention encryption. I can't see anywhere explain exactly what the PIN does. Does it encrypt your data or not?
Famously older iPhones were susceptible to resetting the 'Invalid Attempts to Unlock' counter that the iPhone stored in the Secure Element to workaround the PIN rate-limit, by halting the CPU before it had a chance to increment the value, but right after it returned the pass/fail result.
So Signal could be entangling this PIN with a key from the Secure Enclave, and then trying to securely increment a counter inside the Secure Enclave to implement exponential rate-limiting and self-destruct, but it would be tricky to implement correctly.