I'll try and help out.
Q1: On mine (Mnt Rainier) I have to remove the tube, in order to close the tent. I pull it out completely, and slide it inside the far door.
(so it doesn't slide when I close the tent)
Q2: Yes, I had to remove the travel cover in order to install the annex.
*
Q3: I don't recall. (only got to use mine once so far) It's either the top, or the bottom.
I do know, the very top pieces, the ones that bolt to the mounts, have to be in the correct orientation in order to lock. If they are 180* out of phase, the top rung will not lock in place.
* With the annex on, you cannot fold the tent, at least not very far. My lid opens on my M416, and when I tried to access the trailer w/the annex on, I couldn't. Pic is of my old RTT, but shows how my lid opens.
Since the annex mounts to both halves of the RTT, you cannot do this without stressing the annex.
I'm not worried, because I'll be reconfiguring my set up, to get the tent higher, so I can use the annex to it's full potential.
Hope this helps!
HB