It was brought to my attention recently that the layer 3 backgrounds included in the base are missing palettes and animations. Which was intentional, because it was intended that people grab these things from their respective sample levels (for animations this is the only way).
...but as it turns out, at some point during the development of the base patch, these sample levels were accidentally removed. The ExGFX files should already be in the base though.
This BPS file
contains sample levels of all of the layer 3 backgrounds, from levels 1-11.
In the event that any of the graphics in this patch are different than that of the base rom, use of those graphics in entries is deemed valid. Don't bet on finding anything different though.