Well, first of all, you can't use anything in-game, because the computer AI will not act how humans will act.I guess it's just because I've never tried it, but why would anyone want to "test battle" on a computer program when you could just go to the battle tower or friend code somebody. Wouldn't that be more reliable than some non-Nintendo-licensed computer program?
And again, I'm asking because I've never tried it.
Secondly, computer simulated programs allow you to make a team very quickly without having to breed for IVs and EV train in-game, which is very tedious, especially if you find out the Pokemon doesn't work well.
Besides, hundreds use Shoddy and if there are any glitches or things that don't follow the game exactly, they're not common enough as to affect battlers on a normal basis.