As far as I know, no. You can set the joystick or the yoke to control an aircraft and the other to control a ground vehicle or a boat. The only other way is to manually change the yoke/stick control before you change positions (which is hardly feasible).
Although, some programming functions do allow you to change function modes on the joysticks themselves through the manufacturer's native software. This would not be supported by HTC in any way, shape or form.