This is a tough one. The rules are there, and EK of all airlines are ones to stick to the rules. Even if you paid $24k for an F seat, the same rules apply. I get that and its understandable.
Having said that, having some flexibility is not a bad thing. If the door to the airplane closes at T-15 minutes, why not give the passenger that shows up at 58 minutes a chance to try to make it, assuming the flight isn't full and they haven't given his seat away?
Since its the rules, I don't see how the OP can be upset with EK. As others have mentioned, when cutting it close there are methods to deal with it as far as OLCI or using the kiosks. By the same token, it would be nice if EK had more ability to every-so-mildly bend the rules from time to time.