Enemies are visible in Chrono Trigger as well, specifically so you can avoid them. If you’re significantly over-leveled, they’ll even run away from you, if memory serves. I’m playing through Metaphor: ReFantazio right now, and its solution is to make it so that you can one-shot those enemies outside of battle; and if they’ll actually challenge you, you go into the battle mode proper. That’s certainly one way to skin that cat. Meanwhile, The Thaumaturge (released this year) has a shocking number of similarities in its battle system to Metaphor (and, presumably, Persona), but its number of combats are fairly scarce, in a good way, never really ending up in that situation where you’re super over-leveled, because its leveling system doesn’t revolve around a lot of “number go up”.