There is 0 chance the alternate scenario is played entirely straight and doesn't actually have something new going on. They wouldn't make 5 completely new danganronpa chapters just for the sixth to be the exact same giantess junko plot with all it's reveals you already knew.

>>717468047
Junko cheats in the first game by convicting Makoto in the fifth trial when she knows it's a lie, and in the second game, she even says she only obeyed the rules because it was impossible to counteract the computer's rules. The actual killing game was never the point in any of the games, it was always just a pretext for something else.