If a game doesn't have visible encounters, it should have togglable rates. Like C'mon, we've had that for a long time now (and the Bravely games actually removing the option is just).
that or some sort of limiter whether that's something like having a certain amount of encounters that can pop up per area or something more involved
i've never played it but for example Fantasian has some item thing where you can essentially absorb random encounters and then fight multiple in one go instead of having it interrupt you all the time when you're walking about
another interesting idea that comes to mind that I always remember because i've never seen it used elsewhere is what Exit Fate(a Suikoden-like RPG Maker fangame) did where every time a random encounter is about to trigger there's a button you can press where you can cancel it if you want to by "bribing" them(paying like a third of whatever amount of money the encounter would have given you or something like that), a bit thematically weird bribing something like bats or some other non humanoid creature but a system that feels pretty nice in practice
