Yes, as now with GatEx at Victoria and HEx at Paddington, there may be occasions, such as engineering works, where the route-specific gatelines aren't route-specific.But those Reading passengers can be distinguished from the Heathrow ones, so that's an issue that can be dealt with.
And GWR might want to charge a premium - arguably something they'd be able to do from day 1 of Oyster west of West Drayton, what with Paddington High Level vs Low Level, and the Liz supposed to be taking over all the Relief line services (east of Iver at least).