I don't think it's your assets fault. In addition I think it need solid knowing possibilities of the game engines that we use to avoid this problem. You can't on your side solve the problem alone (games creators needs knowledge).
I just think all the creators you have seen with this kind of problem have not yet acquired sufficient knowledge to deal with it. Or they just don't have enough time/desire to engage this kind of time-consuming glitch hunt (very off-putting).
Ex. In RMMV you can have "unlimited" layers if you try mapping with TileD and the dedicated plugin. But that requires learning to use RMMV and in addition third-party software. It's sometimes discouraging !
Conclusion:
- RMMV + Only Assets = 3 layers = Some problems
- RMMV + TileD (& JS plugins) + Aseprite = Great Success !
