The way I imagine it is that you could have a linear path going through the dungeon from boss to boss with specific trash that is obviously unavoidable. You can add patrols that are avoidable in that path. Clearing through that path does not give you 100% completion. Then branching from it you have several small siderooms (and the aforementioned patrols) and each group can decide which of those they'd like to tackle to get full completion. Perhaps certain seasons will force that decision on you (by spawning the affix mob/pylon/whatever in specific siderooms) but ultimately the route is no longer all about perfect pathing to avoid over pulling.