I can't see a issue because they will simply be displayed as Edinburgh to Glasgow Queen Street via Cumbernauld and vice versa like they do at the moment with with Glasgow Central via Shotts, Glasgow Queen Street via Falkirk High and Milngavie via Glasgow Queen Street Low Level so I can't see why there will be a issue.
Indeed if you look at the CIS link
here, you can quite clearly see how these services are advertised so very very doubtful of any issues.
As to Reading, maybe just maybe the reason why the stopping service is advertised as Ealing Broadway regardless of it actually continuing to London Paddington is because Great Western Railway want to encourage London Paddington passengers to use the non stop services and instead ensure there are seats on the stopping services for stations along the route instead of having London Paddington only passengers use them.
As you can see
here, so I can't see what the big deal is!