Spook, the customized skins are embedded with the terrain.
You can't just make your own skins. However, the "AH Standard" textures can totally be modified as a part of the terrain. Thus, I'm pretty sure the MA will remain the same, but if the CT or SEA features, for example, something like the Eastern Front, the planes will be skinned in Winter camouflage, and everybody will fly in that scheme. This would mean others will be seen that way too.
The textures can be edited separately from the terrain once it is saved into BMPs via terrain editor, thus, this would give a chance for people interested in making new plane schemes to try their hand at it, and submit it to the map-makers.