I have the same dilemma, and I am still trying to figure out what to do. Have thought of the carpet on the hood idea, but I want a clamshell like the Alu-Cab RTT.
I don't like the annex idea at all. I can picture a dog tearing a hole through the fabric and dissapearing; either from boredom, wanting to take off after an animal, or thunder. Sound asleep, you may not hear anything. I'd say either find a way to put him/her up in the tent, or keep him/her in the vehicle. Just hope the pooch doesn't get a need to use the woods: won;t have a way to tell you and there may be a very nasty surprise come morning!