Metaphor: ReFantazio has a mix of real-time and turn-based combat because director Katsura Hashino wanted it to have battles reminiscent of movies and manga.
Hashino explained the reason for Metaphor: ReFantazio's hybrid combat system in a new interview on the Official Xbox Podcast (timestamped here). In it, he said there are "remnants" of Shin Megami Tensei 3's 'press turn' battle system in Metaphor: ReFantazio, but ultimately the latter's evolved into something that lets you blitz through weaker enemies without expending time and resources on them, and still slow down for big, epic faceoffs with more important enemies.
"If you're fighting a really weak enemy, you have this option to use a completely action-based system where you can just knock them out of the park and then move on," Hashino said via a translator. "But if you face off against a more powerful foe, you enter the command battle system. This is going back to the idea of manga and movie-style combat, where you see the main character running around and beating up all the little minions, or the henchmen, just running around knocking them down left and right, but then they face off against a more powerful foe.
"Suddenly there's this faceoff ... and maybe they'll call in their friends to help them and use all of their power at their disposal to defeat them. That balance of the tempo of fast and slow is something that we brushed up in terms of the combat system in our previous games."
The new Atlus RPG has seen near universal critical acclaim since reviews went live this week, and GamesRadar's Metaphor: ReFantazio review is no different, calling it "an evolution of Atlus' best RPGs" and, more to the point of this specific article, praising the combat as deep, strategic, and most importantly, "exciting". In general, the game's combat has been widely praised as innovative, satisfying, and challenging, so it sounds like Hashino and the devs at Studio Zero were onto something.