Short prefixes are currently assigned purely by topological order. While that works fine for final systems, it can be a bit annoying during debugging to keep track of the physical connections.
There are two approaches that I see. One is to add another Broadcast 0 message. The other is to make the register that stores the short prefix available via MPQ. These approaches are not necessarily mutually exclusive. I want to think through the systems implications of these though - it's very hard to accidentally mess things up with the current design, this gives you an avenue to make mistakes.