Alignment of dual Z-axis steppers
All the Prusa-based designs I've seen have only one end stop.  While you are correct that it's theoretically possible for the two Z-drives to get out of sync, it's very unlikely in practice (barring serious friction, binding, etc.).  

But even if it happens, remember that the endstop microswitch is only used to keep the extruder assembly from crashing into the print bed.  The stepper motors do not have shaft encoders, or any other position sensing mech, so if they were to get out of sync, there'd be no way to know this.  

The reason there's provision for a stop mount, on both sides, is simply to make the physical parts of the frame the same.  

That said, it is important to check the extruder support assembly to verify it's level as you build the printer - "level" meaning both supports are the same distance from the screw-drive shaft couplers.