Your sketches are self explanatory, when there is extra stop or level the machine room will be above it.
Two lifts with different heights of working will have machine rooms at different height.
As they are independent lifts and have different elevations, there machine rooms will also be at different elevations.
From aesthetic point of view, if architect do not like it, you can make a dummy room on top of machine room which is at lower level.
You can also buy a lift which does not require machine room at top.