The RTT vs ground tent debate is a long one. Only the debate on oil change interval is longer.
I am involved with an overlanding group here in CO. Here's what I know based on my limited experience:
RTT pros:
Frees up interior storage space
Sets up quickly
Bedding is already in place
Most are well built and can handle high winds and bad weather
Gets you up off the ground- dirt and mud can get scraped off on the ladder, also snakes and ants and bug probably won't find you
RTT cons:
putting a brick on top of a brick makes for horrible highway MPGs
It's a lot of weight put in the wrong place (tent material can make a big difference too- canvas vs nylon)
They don't seem to pack up nearly as quickly as they deploy- pretty much on par with a ground tenter rolling up sleeping pads and sleeping bags and folding up ground tent
A tear in the cover from a low hanging branch + poor weather = soggy bedding
Can't leave camp without folding up tent
Using multiple vehicles as your camping rig is tough
What to do with RTT between trips- leave it on or take it off? They are not easy to take on and off. Need an overhead hoist to do with one person.
I'm about to buy an Oztent. It's a ground tent that costs as much as some RTTs. But because I camp out of my Explorer and my Expedition, a ground tent is easy to transfer between vehicles. Also, I want to park my Explorer in my garage. An RTT is about 10" minimum folded up PLUS the height of the rack it sits on. I don't have the garage door height to accommodate that. And I don't want to have to take it on and off- I have a SAS'd/SOA on my Explorer, it's very tall. And I'm very soft. Adding a bunch of weight to the roof might make the difference of staying on my wheels or not.
As far as body lift vs suspension lift: use body lift as a last ditch means to fit larger tires. I regret my 2" body lift. But because I've got $3000 worth of bumpers and sliders built to the body lift height, going back would be tough. Especially if you go with a RTT, staying nice and low is better.
And as far as sleeping IN the Explorer- no thanks. It's hot. It's tough to keep the bugs out while still providing air flow. You'll wake up with all the windows covered in condensation which will need to be cleaned before you can drive or wait until it clears on its own. And if you get serious about overlanding, you'll pack more and more stuff into your rig (on board water, storage drawers, refrigerators) that will need to either come out and laid on the ground or worked into the sleeping platform design.