That's one of the options I've considered, and I'm not set right now on the whole interior setup, if I did do it that'd be a long ways off, that's more of a pipe dream right now. I kind of like the ide of the fold up side windows, or the fold down side/shelf idea if it was done into the side of the camper. The thing I was hoping to avoid was being outside in the cold/wet trying to cook under a tarp on a stove. If I lived in the west I'd be far less concerned, but my hopes is that this will be used on camping trips across the country, around here in the mountains, the lake, wherever, and the weather's not always going to be sunny and nice out. This is kind of why I wanted provisions for a possible interior space later down the road.
Finding a roof rack capable of supporting the tent and two people is rather daunting. There are two rated at 400lbs but I've heard tales of both cracking under the weight of two people in a roof-top tent. The hard top will definately not support the weight, I'm affraid just to stand on the thing let alone sleep up there.
Another concern was cost. Most roof-top tents are in the neighborhood of $1000. For a college student that's a very large initial investment. The camper is something I can build in the garage in my spare time, a little along as slush funds permit. Rough cost of aluminum I added up to be around $150, plus paneling and hardware. Not that it wouldn't end up costing a significant amount more down the road, but less of an initial investment.
I also want to do something that no one's done before. Something a bit different. If it turns out to be a bad idea, I know what not to do next time, I'd like it to be something that can evolve and I can modify and pick at at make changes on. I'm still a firm believer that real trucks are built not bought, and I admire others' creativity, and it inspires me to try some different things on my own.
I do appreciate the comments and suggestions though! It's flexible, and it's a looong ways off.
Edit - Just caught your lower tent idea. That would be nice if I went with a rooftop tent setup, but again we're back into the $$$ lol