It was not done at the gate. It was done in the check-in area.

EK created a "roped in" area in front of the area where you proceed to the gates. So, you go to check-in lobby, check-in, and then go into this baggage control regime where your bags are counted, checked, and weighed, and then after passing through that new control, you go to immigration, security, and gates. So if you transit within the secure area from gate to gate, you're not subjected to this control. If you leave the airport and re-enter, you get snared by it. As a result, two pax on the same exact itinerary are treated very differently depending on whether or not they choose to leave the secure area on a long layover.

I'm amazed that anyone considers "one bag less than 7kg" to be reasonable.