If my memory serves right the IWHBYD skull was datamined, not naturally found.
As for the painted backdrops in some cutscenes, the choice over a fully modeled environment makes sense in the context of the original release, the game ran at around 720p and you could barely tell. There’s another couple of these skyboxes later (start and end of the final level, “Halo”). I personally miss that in games today, I like painted art