I don't see how this could, in the slightest sense, be cheating. There's no manipulation of game files, no botting, no interfacing with the game whatsoever. TBH, no one would even know you had this on your computer. You can't go to sleep and have the pokemon made for you when you get up. - it's not a broken, all powerful program. Just something to help people, and maybe grow the competitive scene a bit.
I think you may be misinterpreting what this program is made to do.