I'm using the CYBORG 3d GOLD joystick from Saitek.
Throttle in ground position is same as you stated; I've just gotten use to setting the parking brake when sitting at idle. Didn't do it in the 2004 version or other aircraft in FSX.

As for landing the aircraft, I usually bring back the throttles to idle and use the F2 to start reversing the pitch of the props.

Sorry no fixes for your problem, but I thought I'd let you know that I've seen what you've seen....