I don't believe SE designed the game for the current speed run mechanics to occur. A lot of folks may get bent out of shape if you try to consider the balance of the game as it goes against their current favorite method of grinding.
The few things that I can think of that could deter a speed run, such as those found at Amdapor Keep.
1) Once the boss battle starts, all unkilled mobs will pile up into the boss room.
2) Bosses have an HP boost based on the number of unkilled mobs/groups in its dungeon segment. This may result in battles taxing HP/MP/TP more. Better gear and tactics will allow you to "speed run", where other parties may need to level the playing field by killing enemies before the Demon Wall or before that gremlin-ant-looking fellow.