Looking for workflow advice - dynamic game models

Hi. I'm creating models that will move and interact within a game environment. Along with that means that they should not have very specific ambient shadows baked around where objects move frequently. To alleviate this problem, I have relocated most animated parts (and transparent parts like widows). The result is that there is not, for example, a shadow of a door in the doorjam when the door is open. Similarly, relocating glass areas prevents over-darkening of interior spaces. The model going into SP is not the model that ends up in the game, since its parts are all disjointed and strewn about. The game model and display model (eg: for Sketchfab) are assembled and look complete. I think this is a typical workflow situation, but could I be wrong?

When doing vehicles, I try to minimize redundant work whenever possible. An example of that is making tire textures independent of the main body so that they can be used on several other vehicles. All I would have to do is to ensure the tire model is contained (childed) within the vehicle model file. This is nothing new, but maybe not everybody does it this way. I'm just stating my methods because I would like help on a specific thing, but I would want any advice to be informed first.

Another part of my workflow is to give duplicate objects a separate texture. In the past, I had been giving all duplicates of all texture sets only one texture and just give it a very bright color fill, so I can identify it as a duplicate as I work around it. The reason I do this is to prevent weird triangles from being baked into the UVs, especially in AO, and because not every duplicated subobject has the same surroundings. I might have a vehicle with fenders in the back, but open wheeled in the front. Any shadows baked into the front wheels would look worse than any not baked into the rear wheels. Recently, I attempted to assign specific alternate texture sets for each texture set. Where I would have exterior, interior, tire, etc. now I also have clone exterior, clone interior, clone tire, clone etc. My thinking was so that I could instantiate all the layers of the original to the clones. This is all just for visual reference while working, but the final model would use all the original texture sets.

However... this doesn't work the way one would think it should. Let me emphasise that for workflow reasons, it should. Instead, duplicates don't behave the same way and have drastically different results. I suspect it has to do with the multiple things going on. For one, not all UV islands are present in the clones because not all need to be duplicates, so even if I utilize the mesh maps I baked from the original, it won't make sense to the engine it seems. This is probably due to the actual difference in location of the duplicates. For another, the reduced UV islands seems to affect how the mask feature in SP reads the layout, thus not allowing the correct area to receive the desired fill/paint/effects. I tried baking mesh maps specifically for the cloned sets, but the outcome made me realize the masks weren't translating well in the instantiation. Third, this is a very time-consuming, bulky way of doing it, even if it did work. Each layer has to be instantiated individually. I don't think this is really a very well thought out feature, or at least not for what I'm doing.

If you've read this far, thanks! So I guess it comes down to whether I should go back to painting my exploded model the way I had been with only one set for duplicates, or is there a better way to do all this? Ultimately, the desired effect is simple: I want whatever I paint onto a representative object to appear exactly the same on its clones. I don't need the software trying to think I need it to look different just because it's in a different spot, or because the balance of the layout has changed. I want to do this without the clones having an impact on the baked mesh maps, which creates oddities like visible geometry (triangles) represented in the texture where they should be blended.