A ton of the credits scenes use what appears to be the unused mill level accessible by the rocket run soft lock! Did they use it for the scenes? For putting various creatures in there?
Adding to unused levels, was it ever figured out what the web woods beta was used for? Was it testing? It made me think of the Nintendo quarterly exhibitions.
All three games have a placeholder level in ID 00. In addition to those you mentioned, DKC1 has a copy of Jungle Hijinxs with Reptile Rumble's objects under this ID.
It's possible these were once used as test levels had unique level and object layouts, but the layouts were deleted in the final versions and their pointers were changed to duplicates of existing levels.