Not sure how well this can be applied to the jRPG, but I have always enjoyed when something established as a constant, like villages or towns being safe havens, is altered at a point or two during the game. Essentially presenting a pattern of what constitutes a safe haven, and, at a point when the player is presumed to have picked up on the pattern, presenting a level that exhibits all elements of the safe haven pattern but with it being a combat zone instead.
It is almost the case in ff5 when you revisit a former town in-between two "floors" of the same level. The only difference is that you cannot interact with the villagers (but there are no monsters either).
So yes, it does apply to jrpgs
Since you don't have multiplayer in a jRPG (and especially since you don't want a single player game to force its player to hide in a building while the computer fights) you could employ this with a seeming safe haven that becomes besieged, or is the scene of an ambush, and an overpowered enemy has to be delayed or fought off for you to escape. The beginning portion gives the player that sense of being safe, and at the right moment you trigger the trap. Only have to do it once and for the rest of the game the player will remain suspicious of each safe haven.
I can see players wanting to hide. If you make it obvious the threat is high enough and that their gameplay is not just "survival" that could work. For example, it could be a long siege during which the player must fetch food and need to pass through the upper barricades which are in range of the enemy archers. You climb in quick, move swiftly and hope to reach your objective by ducking behind cover.
In ff6, many towns get overrun by the empire, and for the most part, this doesn't change all that much, but one mission focussing on Locke plays altogether differently in a familiar setting. Locke must reach a specific house and finds himself avoiding guards, changing clothes to be disguised, etc. IT really pushes the contrast between the safe haven before and after the empire's assault.
What's even more important is that it captures what a war really feels like from the standpoint of villagers. The player is not fully aware of the war and whatnot, even if its explained through and out. The player only experiences it from the perspective of a resistant and sort of goes through what these inhabitants endure: regime change suddenly reshaping the world they know into something else.
There is actually very few war scenes (Defending Narshe is possibly the most striking example and ony occurs later) and it was refreshing to depict a war from the standpoint of the safe haven.
Thanks for reminding me of that
