Don't really have any good ideas, but .....
- any chance that you inadvertantly pulled 5A fuse #14 or #67 which protect the immobilizer?
I know they are not close by the window lift fuses, but access to the fuse panel is not great and you need to be more like a dentist than a mechanic to do anything.
Don't know for sure, but I imagine there is a risk to pulling some fuses while the engine is running - similar to disconnecting the battery while the engine is running.
My guess is that some part of the computer control has been de-programmed rather than a zap to a major component like the fuel pump.
If so, unhooking the negative terminal for an hour or so and then reconnecting could be worth a try.
Or, making sure all the central locking functions work properly.
Other than that, it might need a tow for the dealer's computer to diagnose and reprogram something.
Too bad you never got the chance to take it for a run to charge the battery up more fully.
Just idling it would not have done much of a recharge.
Just to clarify, the battery has sufficient power to activate the starter energetically, and the engine is turning over - but not catching (or firing)?