I think his overall mangaka history shows that he knows this; the issue with its rarity in most of Fairy Tail is a side effect of his fast pacing with FT. His arcs in the last few years have been very fast, and none of them intended to really set up antagonists that are meant to really be fought later on (with the exception of Zeref, but he's been more of an aloof villain than a "I kicked your ass, try better next time" villain). By the time Mashima sets up the fights between Fairy Tail and the main villains of the arc, he's already set the stage for it to be the climactic moments: the characters are backed against the wall, their only real options being that the Fairy Tail characters find a way to win somehow, or they die/the world gets ruined.
What we have here is a humbling defeat because, quite simply, Yuri, Hades, and Warrod need motivation to become wizards. Maybe Zeira too, given her declaration last chapter.
Actually I'm excited to see where Zeira goes, because I'm wondering if she'll crossover to the main Fairy Tail manga in some way.