If Paddington closed, it'd be a fat lot of good to people trying to get to Slough/Maidenhead/Windsor that Liverpool Street is still operating. You can't build a 2nd terminal for every single station, nor would you be able to preserve enough capacity to operate an unplanned diversion without having a similarly catastrophic effect. It'd be quicker to recover the service to just shut down the affected line so that you're ready to go the moment it's open again.I agree with all that. But I think the point is that that is an argument against trying to have one central station - because one central station becomes a single point of failure that, in the event of an emergency, could totally cripple transport into the city.
Taking the GWML example, if there's a problem at Paddington would it be better to try and squash IC trains into Euston/Marylebone/Waterloo, or to turn every IC train at Reading and run 12-Car s as often as possible calling all-stations to Ealing Broadway? Direct local passengers to the tube, and anybody beyond Reading to Waterloo for the SWR services.
Finally, at some point the 2 routes will have to merge, and that junction will be a critical point. If it fails, you're back to square one - look at the Windmill Bridge Junction power failure for an example.