As far as past travel goes and Random Encounters, the idea is more to help people feel like the world is not just dead. You can't just travel from anywhere to anywhere without the potential of something happening.
I honestly don't want some mechanic where we are forced to manually walk around everywhere or manually walk up to the runes to use them when it doesn't really matter. That to me is boring. If I could click a button and fast travel to someplace with no threat of any kind, or I can walk there manually with no threat of any kind, I would rather be able to press the button and instantly travel there rather than waste a few minutes walking there manually. In that regard, just leave the game as is. If you aren't going to do something like Random Encounters, then the only other real limitation for fast travel should be certain restrictions based on locations and events occurring.
In other words, if they aren't going to build threat into fast travel at all, then the only time I want limitations on fast travel are in places like the goblin Camp after you've killed the leaders. Don't allow people to fast travel back to the Grove or something when there's an army of goblins outside wanting to kill you because you butchered their leaders.
Other than that though, I don't see a need for limiting fast travel if you aren't going to do something to create risk or threat. Don't just limit fast travel to annoy people.
