Puzzle storage belongs on the memerboards. It would be extremely inconsistent, arbitrary, and stupid to allow it on the main leaderboards.

If you have a second file, you can view a cutscene in it (such as the toxic waste cutscene), and use that to store a DCW. This isn't even transferring data between files, it is just setting the "last viewed cutscene" value in the same way that a replay menu DCW does. This was banned without objection, because it requires having a pre-configured file and yet not timing it.

Puzzle storage is even more offensive than that - it is transferring actual flags from one file to another (the storage of the cutscene itself), and yet pretending all the work done to set up those flags shouldn't be timed. Unlike replay DCW, if you delete your file or turn off your console before """""starting"""" the run you won't be able to use it. You're not starting from a fresh game state. Technically that's also true with jinjo manipulation, but that is a pure convenience feature that doesn't change the gameplay, and the extra time taken to set up the file is added back in.

But even more importantly if you had a category that allowed puzzle storage you would also have to allow starting a file with the flag copy glitch, since both do the same thing - allow you to start with data inherited from a previous file. And the flag copy glitch is so strong that puzzle storage is immediately obsoleted, because why only copy the puzzle flag when you could copy ANY flag? Depending on how you define "completing a run", you can get either a 0 second or a ~10 minute time with the flag copy glitch.

But why even use a glitch? Why not just get a file ready to beat the game, start a new file, start the timer, then exit that new file and go beat the game on the existing file? Since apparently progress in another file is fair game.