The rules for EQN2JED are a little strange. If a pin (input or output) is declared as low-active in the pin assignment list, then if the pin is used as a negated term in the equations, it becomes high-active. Confusing? You bet.
Fortunately, in the EQN file for U44, all pins are declared high-active, so Q2 is a straightforward assignment of A2. You could just as easily have said Q2 = A3, but since the GAL uses active-low outputs, it makes sense to keep them all that way. For that matter, any De Morgan equivalent assignment could be used on any of the pins, but since they're talked about as SOP terms, it makes sense to keep the equations looking like that.