Did a bit more tinkering on my "green label" immobiliser box today - i used the data dumped from the box memory to burn a new pre-coded transponder and it looks like it works without any need to add it to the stored key table.
As I'd previously manually added a new transponder the "add new key" process wiped all the old transponder key records (the box didn't come with any keys) so there was only 1 valid key stored.
The software appears to have produced an exact duplicate of the key that was already stored in the key table and both key transponders appear to work, but I can't be sure until I can get this immobiliser box paired with an ECU and get a "OK to start engine" message from the ECU.