Kenne Bell probably just doesn't want to sell you a product that hasn't been tested. I doubt thier product research covered engine swap situations. Besides, the Kenne Bell "upgrade" is questionable, so I wouldn't spend money on it...
I've never studied the difference in the two engines or the ECM's, but theoretically (not concidering functional differences such as fuel injector limitations, fuel pressure available, difference in input/output signals) the ECM should work fine with either engine and vice-verse. During normal operation the "fuel Curve" is based on input from the O2 and MAP sensors. WOT should be the same also. The problem times would be during warm-up and "limp-in" modes.
I don't remember this being an issue in the 1st GEN. With the H.O 3.5 though, you may be looking at some functional difference, like a fuel injector difference. For example, the 3.5 injectors may be designed to work at pulse widths that the 2.7 liter injectors can't so the 2.7 ECM isn't using the full capability of the 3.5 intectors. This would explain why a 3.2 (very similar to 2.7) runs correctly on a 2.7 ECM, but the H.O. 3.5 will operate on the 2.7 ECM, but performs better with the proper ECM.
This, of course, is all opinion. the best thing to do is take the advice of someone who has actually done it and try for yourself. IF you got the money..