That's the function they serve. It's not just a video game conceit; it's an actual portal that connects to other portals, but only when you (or at least one person in your party) knows where they are. Why does it work that way? I don't know, it's magic. This is a fantasy game.
But aren't the netherese portals just a "video game conceit", actually? Right now, only the PCs (including companions) even
notice these portals, let alone use them. Why don't the tieflings use them to travel? Why don't the druids use them to aid in bringing back forage? Why doesn't Minthara (a True Soul, if you want to claim that only those with tadpoles can use these portals) use them for hit-and-run tactics? They seem to exist just for player convenience, and thus are closer to an out-of-game-world mechanic than a true part of the world.