So contacted the guru on all things SCU - Paul at Technozen, who replied:
The BMW EWS immobiliser system hasn't changed significantly since 2004 and I would still consider the original MG Rover technical bulletin to be valid.
Please be aware that this is only an issue if the MGR Keyfob happens to be on the same keyring as the BMW keys, corruption of the MGR keyfob occurs at ignition switch on of the BMW vehicle.
So I'll be taking precautions but sounds like as long as I'm sensible all should be OK.