I don't know if I quite buy that damage will result unless reprogrammed.... It is the final drive and would be the same (probably not to this extent, but you would have to calculate the difference) as running much smaller rubber and/or rim combination. Yes the speedo and odometer would read off and it may or may not shift quite the same, but damage would be unlikely.
With that being said, one of my reasons for the Hypertech is allows for calibration correction for gear changes and tire changes. This should remedy any issues with the change in overall ratio.
As far as the suspension goes, yes you are correct that the air spring is variable spring rate. However, either way you look at it, the overall spring rate for each rear spring "assembly" will be a higher spring rate. Now dampers have compression and rebound valving that is tuned to specifically remove the unwanted motion of the suspension it is apart of. Jeep engineered that valving to be a compromise of ride quality, cornering/brake diving, and travel. One of the key inputs into the valving is spring rate.
Now, you take and increase the spring rate even at the lowest air pressure setting, and the dampers have a much harder time coping with the unwanted movement. Add tongue weight that is applying leverage to the rear axle and causes the motion to start vehicle rocking. This can cause varying tire contact pressure and consequently traction. Now if you were to apply the brake strongly like in a panic stop, you can cause serious brake dive and removal of weight off the rear tires which lifts the tongue of the trailer and induces trailer sway. Bad situation altogether....
So now you add 7 years and 141,000 miles in my case and the wear that has taken place in the shock has reduced it valving ability by causing fluid bleed by in the piston seal assembly. In essence it is a much softer damper. Combine that will increased spring rate, and the above just got worse.
I am a huge fan of Bilsteins. They are high quality with more aggressive valving. They are not harsh, but much firmer than a Monroe, or generic KYB. That additional valving will help control the increase in spring rate. Is it perfect, no because like you stated, the spring rate is not linear. It is however much better than stock and can only improve the vehicles ability to control the truck/trailer combination.
You won't find a better deal on them BTW then www.eshock.com
(Unless they fall off the back of the Bilstein delivery truck.....)