So after some thorough searching, I was unable to find any non half-assed inside tileset mergers. It seems that nobody could be arsed to make a half decent inside tileset merger. What I have done is merge various inside tilesets, remove all duplicate sprites, and organize them by category.
The result is about a 5x size tileset that has all the best inside sprites from 10 tilesets, and since it's categorized it's easy to find what you are looking for instead of sorting through 10 stacked tilesets.
New file is available - note it's not compatible with the other one.
I fixed a few problems, also I added and removed a few things.