Okay, you win on the MASK front. Here's the first 100 tiles of TRAINER:


And here's RACE3:

Essentially the same tileset, neither likely to have been the first level built with that tileset either, but definitely a different spread of masked tiles. What's more, in every level I've looked at the tiles that have masks are those and only those that appear in layer 4. However, the same masking error on the bottom right tile of the window appears in both levels (and persists in castle1.j2t), so they certainly weren't constructed independently. There must have been some external file after all.
(to forestall questioning, I had MLLE add the checkerboards, they're not part of the original files.)