How about splitting London Terminals into geographical groups for ticketing purposes, eg London Terminals West for GWR services to include Marylebone, Paddington and Waterloo; London Terminals NorthWest including Paddington, Marylebone and Euston, etc. Validity to a specific terminus would depend on a permitted route being available, so no Newbury to Marylebone for instance. There would be nothing to prevent a ticket being sold to another London Terminals group at the passengers request, either as the higher U1 fare or by allowing travel on Thameslink/Crossrail where appropriate.
This would at least give clarity to passengers as to which stations their ticket would be valid to or from, whilst still preserving long-standing local options such as Kings Cross / Moorgate. As for the OP's problem, the machine at Paddington would then either be able to sell tickets from other London Terminals groups under the "starting from other stations" option, or whatever it's called, or the machine would not have that function available, as in many other places. Either way the situation would be made plain(er).