What you said is exactly the point of the SB. It changes the acceleration curve in relation to pedal travel. It's not supposed to make your rig faster. I think there's a lot of folks who thought the SB made their rigs faster, which it does not.
With the stock set up when you push the pedal 50% of the way down your not getting 50% of the available throttle. I.E. non-linear throttle curve.
Which is designed to improve mpg but makes for a mushy feel.
SB only makes for a more linear throttle to pedal input.
If you jump between diff rigs frequently it's not hard to notice the throttle/pedal relationship feels unresponsive. 4th gen V6 and FJ's feel like they have more pep compared to the 5th gen. Yes diff motor but same HP.
I'd guess its all to do with trying to get better MPG to meet CAFE standards.