/me doesn't understand. The 4EAT is completely electronically actuated, no? So how is the gearshifter triggering upshifts any different than the TCM triggering upshifts?
Downshifts I can see causing problems, though it is possible to smoothly rev-match downshifts into 3rd and 2nd with left-foot braking and a throttle blip. ( I don't recommend downshifting into 1st - it won't do it anyway unless you're under about 25mph, but it is such a big jump between 2nd and 1st that it's just about impossible to do smoothly.)