I'm definately not the one to ask about 3D, still a noob when it comes to inverting the heli.

my understanding...
as far as flipping the switches, it depends on the programming.... if you program your throttle curve and pitch curve with inverse pitch [-8, 0, 12] and V shaped throttle curve [100%, 50%, 100%] you have inverse pitch linked to your throttle.

regarding the aluminum case for the TREX. I believe you have the correct one. From my experience, they are not the best fit. I have two cases one for each of my REX's, and I had to modify the foam a little to get them to fit better.

-EDIT-

I just had a thought, the tail rotor blades have to be folded in, and then lined up with the main blades in order to fit in the case. Here's a pic of my SE tucked into it's case.