I'll just throw this idea out there: you know how the arcade section of the missions is linked to the real arcade? Why can't some of the missions do that? For a T1 wolver den mission, it will find all the corresponding depths in a random gate and choose the lowest (i.e. the shallowest) one, and then teleport you there. This way, players who decide to go through the main arcade the right way can theoretically join up with the mission-going players (if the party is unlocked).
Criticism?
Missions always have a small tweak, a different special room or a scripted NPC compared to regular levels.
They are similar but not exactly the same.
Also, missions have a fixed depth, and there are only 4 gates. What if there isnt a wolver stratum for your tier? Difficulty is ruined.