Like Allen said, NO PROBLEM.
I have over 100 flights on my AXI with the shaft cut off. I was not sure how important the shaft wheel collar was, but I left it on (in addition to the C clip) to be sure. Like you, I needed the extra room for the Battery.
In the future I will be using a front mount and keep the shaft for the prop. This is so I can use the rear fan units for better cooling.