I’m torn about them. On the one hand they free up the combat design to be as wildly different from the exploration as it wants. Which can result in really creative stuff. Favorite examples are Undertale, MegaMan Battle Network series, and Tales series.
But on the other they interrupt the flow of exploration, the music, you forget where you were by the end of combat and they can be very annoying if they happen to be common or just as you’re about to leave an area. The consolation prize of growing stronger with every battle only helps so much.
I agree these games made big improvements but I still see them as bandages to the inevitable problems that came with random encounters. There’s no undoing the interruption of flow you know.
I think it’s a tradeoff though like I said. Because I don’t know how you can have a combat system as cool and creative as say Undertale (blending turn based and realtime bullet hell) or battle network (blending turn based, real time and card game) without it being completely separate from the overworld.