What is nice about the Commander is you already have a transom. You only need to install the block that is made for it or you can make your own block out of wood if you are a do it yourselfer.
Just about any transom mount TM will work with some modifications such as hooking up the cables as you would rigging a rudder and using the foot pedals for steering, or use a control handle extension, but that limits having anything sticking up such as rod holders on the crate.
I cut down the shaft and rigged up an old 30# thrust motor I had lying around.
The hardest part is already done when they designed the Commander with a transom.
Just one more cast!