i wasn't really planning on doing any special modification of the terrain or scenery in these areas, so there wouldn't really be a visible border, except for some sort of warning signs, or a guard of gatekeepers around the perimeter. not a whole lot of difference between getting killed by a gatekeeper and getting killed by their boss - either way you quickly figure out your outclassed and in over your head. so why bother with gatekeepers?
having NPCs running away would probably look silly after the first few times. why does there always just happen to be an NPC fleeing every time i discover an epic encounter area?
landmark warnings seem to make sense. landmarks would be similar to the hide door seen on the hut in the screenshot below, perhaps with a skull and cross bones or something like that painted on it.
place a circle or bbox of landmarks around the area.
but then you need to tell the player what that means somehow. it could be a dialog option, but you only really need it once. its could be a loading screen hint, but there are no loadscreens! : )
it could be color dialog you hear when near NPCs, but again, you only need to hear it once, not ad nausium, like "I used to be an adventurer like you...".
or you could just let them figure it out:
"whats that over there? looks like some sort of landmark. but what are these markings on it? looks nasty - whats going on here?"
the player moves a little further into the region, and gets an epic encounter. and then experience becomes the best teacher:
"ok, i encounter really nasty stuff every time i go past one of those weird landmarks. they must mean "bad new ahead!" <g>.