Gearing, or re-gearing, a 2.7 auto VS. 2.7 MT

I've been searching, & still unsure. From the calculators & charts I'm using, my 2013 Reg. cab, 2.7 4X4 W/ orig. 245/75/16 tires, (30.46" dia.) & orig 4.10 gears, & auto trans. runs 1900 rpm. @ 60 mph. The exact same Taco, 2.7, 4X4, W/ orig. 245/75/16 tires & orig 4.10 gears, except with a 5 spd. manual trans. runs 2171 rpm. @ 60 mph. A difference of 271 rpms. more with the manual trans. I've already went up to 31.61" tires, & that lowered my 60 mph. rpm from the orig 1900 to 1830 rpm. Now back to the calculator, if I re-gear from my orig. 4.10 to a 4.88, with my 1.2" taller tires, my rpm. @ 60 mph. will be 2179 rpm, only 8 rpm. different than that 2013, 2.7, 4X4, 5 spd. manual was running straight from the factory. If the Taco W/ 5 spd ran 2171 & wasn't screaming at hwy. spd. mine with an auto & 4.88 gears, shouldn't be screaming at 2171 either. I'm afraid I'm missing something, It seems if I go from 4.10 to 4.88, It'll seem like I'm screaming, but if 2171 isn't screaming with a manual trans. 2171 shouldn't be screaming with an auto trans. Any help, or clarification, appreciated.