As long as you have completed your replacement of the Pirelli seal and perhaps some insulating strips around the door to seal out drafts, the functionality is fine.
I like the ability to open just the top door for fresh air (using the screen of course to keep out flying insects) while keeping the lower part closed. The design of the upper/lower system required this set up and it works just fine. You don't have to duck down or be 3' tall to enter your camper or to get out.
The bottom half of the Alaskan may have some SPLAY to it, which means it is wider at the top of the loser section than at the bottom. Look at the steel angle iron where the rear panel meets the floor panel for a crack at each corner where it is cut out for the door. In addition, if you look at the door when closed and see that it does not seem even from top to bottom, that is further evidence of some splay. It may also make a solid closure of the door lock mechanism as well.
If you find your camper has this problem, the easiest way I know to address it is to loosen both rear tie-downs to the truck, put your camper jacks at each rear corner and begin to EVENLY raise the lower section. Do this EVENLY until you can see that the door now fits against the jamb equally from top to bottom on the lower section. Now is the time you hammer in a couple shims, one on each side right where that angle iron is located. Next, when you lower the jacks if the splay has been corrected you are good to go. If not, raiser it again and hammer both in a little further. Now, lower the jacks and if the splay is gone...Mission Accomplished! You can cut off the ends of the shims or leave them. However, this is something you will probably have to do at least once a year and more if you use the rig a lot or water gets to the shims. Just keep an eye on the door-to-jam alignment and a couple shims stored in your rig and you should be OK.
Tricks for attaching gear, etc. to the outside of an ATC?