The way we design aircraft and liveries is by splitting the aircraft into two different objects. One being the base model and the other being the actual airline livery. That way we can have multiple instantiated aircraft of the same type in game, all with different liveries but sharing the same base object. This is of course much more efficient than using individual objects per livery and it allows us to use a very high texture resolution (up to 4096x4096 px) without having to worry about graphics memory size or performance issues.
For example, the vanilla 737 models (-600 & -800) can be fitted into just three different texture files containing 11 different liveries, with multiple parts being shared in between the different liveries. If we were to have these parts unique per livery, we would have to create a single texture per livery which would both take up memory space and add additional draw calls (basically reduce rendering performance and ultimately lower fps). Therefore, the current modding system is adapted to this design since it is very rare to have custom painted wings and horizontal stabilizer, the decision was made to keep these out of the modding files so that any modded liveries could work with the existing system.
Another reason for using this system is to reduce loading time as Airport CEO will have to create a sprite from the modded .png from the mods you have selected. Each texture file will take an X amount of time to load depending on its size so it is favourable to keep these small.
A good thing is that there is a way to get around this by editing the liveryData.json file. It is just a list of parts and instructions how to read them from the .png file and place them into the livery model. So drawing a new part to the .png file and adding it to liveryData file is of course an option although it might be a bit hard to get the local position right in game.
I hope that makes sense anyway. 
Livery and base model
Part of the 737 base model
The vanilla 737-600 liveries and engines (which are used on -800 as well) tightly packed.
The new E170 with all parts packed into on a single texture file.