Returning to stock tune resolved the problem, it shifted as you would expect, including light throttle upshifts at low RPM. Seems like increasing shift firmness with the Hypertech also cranked up the shift points, which is some pretty wonky behavior.
I wanted an SCT tuner anyway to try to resolve an annoying harmonic vibration at idle, so I picked up a used X3 3015. With that tuner I was able to adjust the firmness individually for each shift, in the same way the Hypertech worked on my F150, without affecting the shift points.
For whatever its worth, I bumped the 2-3 and 3-4 shifts +20%, and they're fairly solid and crisp without being rough or annoying at all. But even going +25% on the 1-2 seemed to make no difference, it's still very soft. I'm guessing there's some sort of torque management at WOT, although why you'd need that on the 4.0 tractor engine is kind of a mystery to me.
Incidentally, the canned SCT 91 octane performance tune really woke up said tractor engine. I made the mistake of standing on the throttle from a dead stop with the windows down (listening for ping), and when I got wheelspin, I figured, "Eh, it's early in the morning, dew everywhere, tires must be wet" and by the time I realized they weren't, the interior was filled with smoke. Ooops!