I wonder how programmable it is... Assuming it's not programmable would be an argument not to use standard encryption algorithms.
It's probably easier to use a standard algorithm in a way that can't be attacked by this machine (e.g. use AES-256 with a properly random key) than it is to create a non-standard algorithm that doesn't have vulnerabilities.
AES-128 is the norm. No NSA supercomputer should convince you to use AES-256.