The good news is that the engine MIL problem is sorted and the car rushed through a successful MOT. I wish I could claim full credit for analysing the system and explicitly tracking down the fault - but I cannot.
Given the scenario described in my original narrative, it was clearly linked to the alarm system. What I did not say in my narrative was that, as the car only comes out of the garage occasionally, I have fitted quick connectors to the battery and disconnect it when it goes away (might be a drain to earth somewhere as the battery fully discharges within a 1-2 weeks). I know disconnecting the battery can cause some issues with the alarm / immobiliser system so I left the battery connected, used the OBD to look at any fault codes (of which there none), but did a 'Clear all Codes' anyway. The engine MIL operation was fully compliant with the design thereafter, so the answer seems to be don't go disconnecting the battery!