It would be helpful for us if every generated texture atlas didn't have the exact same filename (so, for example, we could more easily identify loaded textures in a crowded scene and clean up dependencies).
So, in tk2dSpriteCollectionBuilder.cs, I'm changing the line that sets the name to this:
string texturePath = gen.atlasTextures[atlasIndex]?AssetDatabase.GetAssetPath(gen.atlasTextures[atlasIndex]):(dataDirName + gen.name + "_atlas" + atlasIndex + ".png");
Which turns an atlas0.png into my_collection_atlas0.png (where my_collection is the full name of the sprite collection)
I basically just wanted to sanity check and make sure this was an OK thing to do and wouldn't cause unexpected problems! Seems safe but I don't mess with the tk2d internals any more than I have to.