So the scenario is the following: you bake out your chamber while your manipulator is inside and you cover it with a Mo dummy wafer, right?
The Mo has probably two functions: a) protect the manipulator from picking up the dirt that you evaporate from the chamber walls b) not being a source of contaminants itself. Molybdenum chemisorbs oxygen species quite well so if e.g. water from the wall ends on it, it might be bound chemically. Also, it does not evaporate a lot itself so it's not a contamination source.