Asking for your passport in the domestic security check seems daft I agree. I'm not familiar with LGW but from your description it seems a bit of a security loophole if Customs want to check international passengers' passports yet they can easily go through the domestic channel thereby avoiding their passports being checked?? And if the domestic channel includes passengers to Northern Ireland, does that save the IRA forking out for fake passports every time they nip in and out on a bombing run?
Asking for your boarding pass however is to ensure only passengers avail themselves of the duty free - not airside staff who aren't going anywhere. Meanies!