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Back to Paddington; if you go by how the station(s) is/are arranged, the Hammersmith & City platforms are 'part of' the NR station, in that the platform numbering is one (the LU platforms are 15 and 16) plus the ticket gateline is shared (one gateline for platforms 10-14, although it is possible to get to these platforms without using the gates on the bridge where the LU ticket machines are located), not to mention the physical next-ness of the station - though I guess this is the same with other stations. The Bakerloo and District platforms are a separate entity, with a ticket gateline where the only trains available beyond it are LU, and separate platform numberings. NR's 'Stations Made Easy' kind of has separated the two up by refering to the H&C as 'Platforms for London Underground Hammersmith & City Lines' while the Bakerloo and District lines is shown as 'London Underground Paddington Station'.

Geographically though... the Bakerloo Line is (or looks to be at least) under the main NR concourse, facing (roughly) the same direction (so anybody doing the H&C-BD run is effectively running the length of the Bakerloo platforms) - so if there was an entrance to the Bakerloo line platforms from the Hammersmith & CIty lines, would that finally make it one station? (not sure if it's physically possible with the way the station building is built though...)

It would be handy for a zone 1 challenge, but wouldn't make any difference for a GWR as even if you ran from Bayswater to Queensway, you would still pass through Paddington on the Bakerloo.