Lyndon, I don't know if the Mk2/2.5 behaves the same as a Mk3. I've never noticed that with our Mk2.5, perhaps it's never been unused long enough, but when our Mk3 stood unused for more than maybe 3 weeks it would go to sleep and not respond to the remote. Unlocking mechanically would set off the alarm which was cancelled after starting the engine (or at least turning on the ignition). Once this had been done to wake up the car the remote would work normally again. This sounds very similar to your experience. On consulting the User Manual I found this was normal for the Mk3.
From the OP's first post I would say his car has definitely gone to sleep and just needs the procedure above to wake it up but that, of course, means getting the mechanical lock to work.
Also, to answer his question, the car going to sleep does not disable keyless start and does not require the fob to be placed in the emergency start location on the steering column. I can verify that as our Mk3 was keyless start.