I have seen CT's made with only a single door in the back. If you are ordering one you might check into that.
IMHO. If you get one off the lot with 2 rear doors, definitely get rid of the factory lever lock system. If you want to keep the lever latch for additional security while on the road, you would need to make a way to lock it where it is inoperable while you are occupying it. You could use a latch system like this on the second doors to secure it closed.
http://www.amazon.com/Stanley-757029-Zinc-Plated-Chain/dp/B000FKBP7M/ref=zg_bs_511280_20 I would use 2, one top one bottom. A standard RV style lock should take care of the first door.
http://www.amazon.com/Travel-Trailer-Flush-Deadbolt-Keys-Colonial/dp/B00768Z37E/ref=pd_sim_sbs_auto_2 This type is generally made for 1 1/4" - 1 1/2" thick door. My door was 1" so I had to shimmed with aluminum diamond plate.
Something I would suggest is to install a secondary escape in case you need to evacuate in case of an emergency and you can't use the doors. RV trailers have escape windows installed in them for this purpose. I've never had to use one and hope I never do. But it gives me some peace of mind knowing that I am not trapped.
Good luck and looking forward to your build.
Earnest