Right, so as you say, declining sales up until a few years ago may have pushed Toyota to consider dropping the 4Runner. That's nothing to do with fuel economy, other than the fact that sales of low MPG vehicles drop like crazy when people can't afford the gas to drive it (e.g. 2008).
These trucks are so old school that it would take hardly any new tech to bring it up a few MPG. Remember, no particular vehicle has to meet a specific target because it's about average of all vehicles they sell. Toyota could sell a 4runner getting 4 mpg without penalty if it fit in their chosen compliance strategy. They sell more than enough extremely efficient cars that their (corporate) average fuel economy will be plenty healthy with minor improvements to their BOF trucks. Toyota of all companies is probably in the best position to sell old-school BOF trucks because people are happy to buy their hybrid cars

(To be honest, a simply mild hybrid 4runner, with the extra torque like the new RAM V6 will get, would be fantastic).
I really don't see any way to support the assumption that CAFE will kill the 4Runner, and that's partially because the standard was specifically designed to avoid killing certain products. Think of it this way - higher MPG means it's less likely that 4Runner sales drop the next time gas prices go up or we hit a recession (it was drastic in 2007-2015!) meaning Toyota is less likely to give up on it after the 6th generation.