There are two different situations- one is painting different parts with different colors, the other is painting over previous paint with another type of paint. You seem to be talking about the first. Ordinarily this is okay. However, there may come times when you want to clear coat parts or all of the model- say to seal decals, or to put down a gloss coat in areas before decaling (to prevent silvering). Since clear coating is a common procedure, I recommend that you give some thought to paint compatibility.
Now, paint compatibility is a can (or bottle) of worms. In the old days you needed to worrk about only three types of model paint- lacquers, enamels, and acrylics. Now, each company seems to be developing their own, unique chemistry. Only sure thing is to run tests. Again, as long as parts are completely dry, two can be painted with different types of paint, and be touching, and they will be okay. However, there will be so many situations (weathering, washes, clearcoats, etc) that you may want to overcoat that you should be sensitive to this problem .