I haven't done much touring yet, but I have an LHT and want to discuss a few of the issues that OP brings up:
Brakes: For me this is the weak point. I don't need disc brakes, but the low-end cantis are not very good. It'd be nice if Surly included nicer brakes.
Tire clearance: The LHT has plenty and is available for 26" wheels. I have a 700c model and no issues with it.
Low gears: The LHT has a a tiny granny gear and a wide-range cassette. I'm fairly certain it's a lower gear than what you can do with a Rohloff. I rode in North Carolina on vacation. The Blueridge Parkway itself has long climbs that aren't terribly steep. Once you get off on local roads, well, anything can happen. I did fine climbing with my stock gearing.
Rohloff hub: I'd love a Rohloff, but can't afford it now anyway. You can install one on nearly any bike with a chain tensioner, but I think you'd like a Rohloff specific dropout. There are a few manufacturers who offer that, but it is a small market.
Gates drive: I'd like one for a city bike, but I'm not sure it's ideal for touring. The "cutout" frame required could potentially make for a weaker frame. Replacement belts along the way could be an issue. Replacement chains are plentiful. If you do have a Rohloff driven by a chain, chain maintenance becomes simpler.
S&S Couplers: These things are expensive, that's why so few production bikes have them. That said, you can have them added to many frames.
Drop Bars: Nearly all touring bikes sold in the US have drop bars.
Fork Rake: Most non-disc touring bikes have nice fork rake. My LHT does. Most disc forks do not. I guess it's a design issue. Disc forks need to be stronger which makes them less flexible, therefore less comfortable.
Touring bikes are a niche market. The major manufacturers are trying to hit a price point. It always leads to compromises. You can buy your dream bike, or have a frame custom built, but it costs a lot more. It's still a lot less than any new car.
People have been touring on bikes of all shapes and sizes, from custom built high-end kit, to $200 big-box store bikes.
Oh, and what the big deal spending $3500 on a bike when you put $600 worth of panniers on it.
