Do you want to paint your fliers the same as the rest of your army? Given that
40k forces can be made up from a number of different force elements, or in the case of the Tau, different Cadres, there is fluff support for whatever you want to do.
The flier could be organic to your main force, it cold be from a different cadre but using the same general colour scheme because its in the smae theater of combat, it could be from the same cadre and painted differently because its an aerospace asset rather than a ground asset, or it could be from a different cadre and painted differently because of a number of reasons. In my view you should never try to use fluff as a concrete reason to do anything. Paint your models the colour you like and then come up
wth the fluff to support it