Hidden mechanics are not unusual in RPGs. Sometimes there are portions of a game that a player should not need to actively worry about or perhaps it could be part of an illusion. Still, sometimes knowledge of these mechanics can aid a player. In service of this, here are a few mechanics that may or may not be obvious.
In Team Asano's later series Octopath Traveler, each area is given a Danger Level to signify to the player what level they should be at to survive the enemies within. Final Fantasy III for the DS actually has a similar system, albeit more silent and more punishing. Each area has a "Danger Level" assigned to it and the player's levels in relation to the "Danger Level" influences the encounter rate. If the party is overall below the Danger Level, then the encounter rate will be increased. Once the party reaches the required threshold, however, the rate begins to decrease until 6 levels ahead of the area. This is especially apparent with the Alter Cave: You'll run into more enemies at the beginning of the game than you will if you were to go back later.