The improvement is purely due to the increase in thermal efficiency. The math is accurate. You're of course welcome to verify. The assumptions I used are .45 coefficient of drag, 70mph, .008 coefficient of rolling resistance, 30sf frontal area, and 4,500lbs, 114,500BTU summer gas, .95 drive-train efficiency. If you move from .25 to .37 thermal efficiency it matches the increase in mpg. All else is static.
If the current 4runner gets 21mpg highway - and I've done better at 70mph - so I'm pretty confident in that number. There no reason we couldn't get 3-5mpg with a 6spd and higher efficiency engine. If an F150 can manage 26 with a turbo, a 4runner should be able to - atkinson cycle engines are significantly more efficient than Ford's ecoboost engines. Of course Ford manipulates the rating so a 26mpg ford in the real world is probably 23 comparable to a Toyota epa rating. I agree that 28.9 is outside the realistic range unless we gen an aluminum version that's 3,500lbs. Or a diesel.