No, I think it applies for both windows, 2016 and 2017. They can exercise the clause from 16 june to july 16 in 2016, then it closes and reopens again in the same dates from 2017.
I think it's net, because Chelsea's offer is 6 mil and Morata wants 7/7.5. They won't be offering him 6mil gross which is 3m net, his current salary basically.
Chelsea offering 6M net would make him their 2nd or 3rd highest paid player behind Hazard and Costa. Doubt thats true especially the part that Morata asks 7M-7.5M which would make him close to Hazard or maybe even 1st. Doesent make sense unless it's gross