Yes, that's correct. And, there are no options to the right of the configure action box that relate to the controller. The only way to map the actions to the axes is to use the presets. But, all the presets for helicopter controls use Z-Rotate for the pedals. I believe Heli-Kit differs in that it uses Y-Rotate for the pedals. Everything works appropriately except for the pedals. The cyclic and collective inputs are correct when I use the Flight Link helicopter presets.

I am having the same problem with the same helicopter controls. I've attached screenshots of the Arma 3 setup screen for Heli-Kit and the Microsoft screens. I annotated the axes with what controls they are associated with.