How to wire an Air Conditioner from the disconnect when exposed to physical damage?
I assume you mean AC Condenser Unit : You can run EMT to the unit - typically a flex conduit cable is used (almost all installations I have seen use a flex conduit) but you can use emt if you like.

From your LINK   356.10 Uses Permitted: 


  Where flexibility is required for installation, operation, or
  maintenance.


Use the Flexible Conduit to attach your condenser, connect your motor - use a strain relief on the physical wires and wire ties as well to limit the vibration of the wires.