Moral dilemmas
The Minor realms within the Inn presented Lex with a tricky predicament. They had completely fused with the Inn, as was apparent from the fact that they traveled from the Origin realm to the new Midnight realm.
He could also place their entrances freely as he wished. Even actually inside the realms, he felt like he'd gain complete control sooner or later. For the empty realms, he saw no issue in doing as he pleased. But for the Minor realms that had civilizations, such as the one that had so boldly attempted to invade the Inn, Lex felt like he was in an awkward situation.
Even if he wanted to ignore it, and treat it as if it wasn't his responsibility, the knowledge that the entire world for countless living beings was under his control made him feel… strangely uncomfortable, and burdened.