Maybe Makoto isn't his world's Beholder after all. It could be someone else.
Naegi reminds Ascheritt of a former student
At the end of Chapter 3, Zerase seems to know what's Ascheritt is doing and that is to make way for Makoto in case if he wants to join the Realmwalkers. Zerase warns him not to let his past cloud his better judgment. We also get this:
Zerase: Do you want that boy end up like the other one?
It may look that Makoto reminds Ascheritt a lot of someone he knows and something bad had happened to him.
The Primal Union's goal
They felt that there are too many alternate universes that they make their prime universes less unique and see the parallel universes as unnecessary additions. They're destroying the parallel universes for the sake of the core universes, but they're unaware that they cause more harm than good. The damage they do will be too great and permanent.
The Unknown could be a former Realmwalker
At the end of Chapter 3, Lion made it clear that the Rune Crystals are specifically for Realmwalkers. So how did the villains get their hands on the Rune Crystals? It could be that a fellow Realmwalker has gone rogue.
The Unknown's Identity is an alternate version of Makoto himself
It could be a scrapped concept of Makoto. His series' Word of God
mentioned that Makoto was originally going to be the Big Bad
for Super Dangan Ronpa 2, having descended into Despair.