There are no reasons for the colourscheme of the aircraft on a specific route. Some aircraft have cityjet livery and some have air france livery. The aircraft are used/rotated as required over the entire cityjet network with no relation between livery and route. As far as I am aware the aircraft will not be all painted in the same (cityjet) livery.
Cityjet used to operate all their routes as "air france by cityjet" and all the new LCY routes are branded "cityjet for air france". If I recall correctly the LCY-ORY and LCY-DUB flights already existed and remain "air france by cityjet".
ScotAirways are flying on wet lease for cityjet with air france flight numbers (as all cityjet flights have). So for the pax all the flights are air france with air france tickets, not really confusing I would say...