What happens? I assume it does interrupt the cruise function - maybe it's too early in the morning, but I can't picture the motor both driving ahead and braking to send current in the other direction, at the same time. And then when you release the regen control, the motor returns to cruise control? I'm not sure, I might like that.
Interesting that the Phaserunner itself apparently doesn't support cruise control, as some other controllers do. Looks like it's designed to require CA3, so full function on stuff like interaction with cruise control depends on running everything through CA3.