I personally like the lift top a lot. I have been pondering the idea myself. Personally I really like the Unicat version, but I doubt I would ever be able to afford that. If it is not obvious already, I am considering a much larger vehicle for my personal needs. Further I am not looking for an off road vehicle, so I think I will likely go with a Volvo myself, and that large of a truck has a lot less in the way of weight restrictions.
If you check out the windows in the campers where the tops go up and down, like the Alcan, and there was another linked early on, as well as that of the Unicats, (the few that have windows) you can see that the windows are fairly dramatically set in (looks about three or four inches) I presume this is done for the clearance you mentioned.
Gray water... My first thought on that would be could you use a battery heating pad? My wife and I are thinking seriously of moving up to Alaska, and one of the things that you have to do to winterize the vehicles is install a heating pad around the battery. Could you, perhaps, put something like that on, or even a tranny heat pad glued to the bottom? This would keep it liquid enough to drain, and of course it would be switched so that you do not need to run it all the time, if the tank is gravity fed you could even let it freeze and simply thaw it out when ready to dump. I do not know if that is possible or if that will all work out, but it seems logical in my mind. (Pardon me for not being an expert Joaquin. None of my vehicles have ever been on the discovery channel after all.)
Now, with the roof, someone posted up a lift intended to raise and lower a bed in the back of a toy hauler camper. Have you considered using something like that to simply raise the entire roof? If you are going to lift part of it, I would think that such a lift as the earlier link might be a great way to simply lift the entire roof. Folks have told me lifting the entire roof would be more difficult than doing what your original plan called for, but I personally do not see it. It seems far less complicated.
The solution to your first problem (the door) would be to add a two piece door, of which you can open the bottom alone, or open both. This way you can open up while the top is still down.
Last thought for you, I wanted to second a previously mentioned thought of using the roof rack to hold the Mt. Bikes. Fold in half or not, if you put those things in the hall way of the camper when shipping, and then out on the roof while driving, it will a lot a greater amount of space for things that need to be indoors while traveling, even more space for clothing.
Well, none the less, I have learned a lot from my conversations and speculations, and likewise I have learned a lot from reading about your ideas.
Good luck!
Brian