The law is very clear on this tbh. Direct commercial passenger flights inbound from the UAE were fine until 1300, but prohibited from 1300 onwards. From 1300 the airline can still operate in to the UK but it would have to be cargo only.

The prohibition applies to flights landing in the UK and not departing. So airlines are free to fly direct passenger flights still from UK->UAE at any time.

The EK flight could have operated to MAN on schedule landing before 1300 with passengers, and departed at any point later with passengers. Going forward EK can still operate flights in to the UK without passengers but with cargo, and take passengers back to DXB.

Apologies for the detail. Tbh I just wanted to pick up on your point that they may have had to depart by 1300.

There is more information on the thread in the coronavirus board for UK arrivals requirements.