Encounters are, in my experience, something planned (as would be the case for a map & key type dungeon) or something determined randomly (as would be the case on a regional random encounter table).
These are generally things that I’ve crafted ahead of time, or may procedurally generate with tables, depending on the game. Given the way I run even trad games, they also may be something I make up on the fly, as needed in play.
But I don’t tend to think of encounters as like a unit of play for many of the other games I run. It just doesn’t make much sense given how those games work. So in those cases, I don’t think the idea of bypassing an encounter makes sense.