Sleeping in the vehicle is fine when by yourself and I've done more than my share on surf trips to Mexico and up & down the California coastline, but the wife wants more room and comfort and you can't beat the ease of setting up and taking down a RTT with a real foam mattress, pillows and sleeping bag, all laid out, waiting for you inside. Also as you noted, tents, sleeping bags and pillows take up a lot of room inside the vehicle. This leads to decision making upon what to bring and what to leave behind on a trip. A RTT has this all stowed up top.
I concede that I don't like my CG being so high with all that weight on top and poor gas mileage. Nor can I drive through a carwash any more, along with limiting some parking garages.
As far as price, I consider that a personal pain threshold. For some people the purchase of a RTT is not much more than the change they lose in their sofa. For others, they have to really consider the cost verses the benefits. For me, cost wasn't an issue and we love it!
I went through the same thing when I purchased an F350 Crewcab with the 460ci motor. My first overlander I built. Before even getting it I knew I had to reconcile really bad gas mileage and I was never going to park front and center anywhere, I'd always be parking in the back of the lot. Knowing and accepting that when I bought it, I love it! It was awesome... until I rolled it...

Then I bought a Landcruiser and built that as my second overlander. Great rig!

And NOW I have this GX, the best so far!!!!

The only time I have concerns is any type of extreme off-roading (read: rock crawling) because of the 150 lbs plus weight up top. But I didn't build my rig as a rock crawler, I built it as an overlander, which it does very well! (Which remindes me, I still need to post our trip to Maine on my build thread...)
I agree, there's a trade off in all of this. My biggest complaints about RTT's are price, weight/COG, reduced fuel economy/wind drag, and the fact that they compromise your entire roof rack.
Price-we can complain about this in regards to a lot of the products available in this niche market, it is what it is, but that doesn't make it any more bearable.
Weight/COG-An extra 150 lbs 6-7" above your roof line certainly changes handling characteristics both on and off-road and it compromises it most in off-camber and high-speed maneuver situations, clearance both for overhead on the trail and in regards to garages is an issue as well.
Reduced fuel economy/wind drag-Some are better than others in this area but regardless you can expect a reduction in MPG and added wind noise.
Rack space-That $1200+ roof rack you bought to carry your $3K+ RTT no longer has room for your MaxTrax, cases, Rotopax, etc.
Ground tent-You still have to set it up, break it down, carry around all of that gear broken down which takes up a lot of extra space. OZ-Tent for example is a fine product but they are huge and heavy even when packed and that has to have a place to ride which compromises a lot of space on your rack. Adding an extra 15-30 minutes to setup/breakdown my camp isn't something I want to mess with every single day. Cots are nice and keep you off the ground (misses hates sleeping on the ground) but again it's another bulky item added to your cargo that needs to stored and setup. The biggest benefit is that it doesn't compromise the mobility of your vehicle when setup.
Off-road trailer-Expensive, expensive, expensive. They introduce an entirely new liability which is towing. Added spares, added weight, added responsibility both on and off-road. Some are setup and ready to sleep simply by opening a door and others still require setup time. They change where you can go, how long it takes you to travel, your fuel economy is reduced, and it adds complexity to the trail and how you attack that trail. You can set it up and then leave camp not compromising your vehicle when in use.
Interior sleep platform-Takes up a lot of space only to provide you a small amount of sleeping space. Requires completely altering your interior layout in favor of providing one added benefit (lose seats and cargo space). Sleep systems are few and far between and usually require you to buy pricey one-off systems or you have to build your own. Sleeping space provided usually is small and still needs to be converted and setup and broken down each night/morning and you still have to store your bedding somewhere as well. No added exterior weight or size keeps you streamlined and stealthy.
FWC, AT Habitat, off-road trailer, sleep system, ground tent, hammock, we've tried them all over the past few years and they all have their shortcomings and their merits. Ground tents are always going to be the cheapest and the most versatile but of all of the options out there they have the most setup and break down time associated and will take up a lot of space when stowed. When camping solo I definitely prefer to sleep inside of my vehicle, but it's definitely not as ideal when the misses comes along. I had the highest hopes for the off-road trailer and it ended up being the one I liked the least, too many drawbacks IMHO. If you have a truck it's hard to beat the benefits of a FWC or AT/GFC but of course they present their own added compromises as well and lets not even mention the cost haha.
If my GX were a dedicated weekend travel/camp vehicle then I wouldn't be as opposed to the idea of a hard shell RTT as long as it fit somewhere covered/enclosed when not in use. I don't want to mess with removing the RTT and storing it when not in use and there's no way I am going to daily it with that on thing top. The GX is more of an overland vehicle (man I hate that term lol) so you're right that the COG and clearance aren't as much of an issue since you're likely not tackling any super aggressive trails but it still isn't my favorite. I haven't figured it out yet with the GX and I am not sure which direction I am going to go but I am leaning towards the Goose Gear sleep platform (whenever that ever comes to market). Until then, I will likely sleep inside via my makeshift layout or I will drag along a ground tent.