Let's say I make a signpost metatile on my primary set on the middle layer. Its bottom layer is grass or something.
Now I have a secondary set that's got some special orange grass, and I put that same signpost in the secondary set on top of that orange grass.
Then at some point I edit a pixel or two on the signpost on one of the two sets, but at this point I've forgotten about the identical signpost on the other set.
I have no idea how easily doable a warning when two metatiles (16x16) are almost identical but not quite would be. A "hey are you sure this is intentional?" sort of thing.