How Low is too Low:
We call Zone 1 AeT minus 10 down to AeT minus 20
We call Recovery Zone below AeT minus 20. The fitter you become the less aerobic benefit there is to training in this Zone.
You are correct that the neuromuscular stress of running uphill is lower than on the flats or downs. Whether or not to spend more time in Z3 on uphills all depends on your intended purpose for that workout.