Well yeah, exactly... every 'scort layout worth its salt already took double Omega. You'd be nuts not to.
AP DOffs don't really have anything to do with the cooldowns, it's just that you can get more uptime out of the higher AP:O rank so you're getting a bit of a burst and defense increase overall. In all honesty you can already emulate having AP DOffs without actually using them because like you said, it's always been possible to slot double Omegas. Play smart and use your copies appropriately and the DOffs aren't even really necessary.
There's also the option to free up one of the Omega slots, but to be honest that's quite a massive opportunity cost in terms of DOffs on the part of the 'scort that you can take advantage of. He still doesn't have more Omega uptime than he ever did (just more cannons) and now he's eating into his SDOs.
in my opinion, its EPtX damage control doffs, AP doffs, or BFI doffs on a escort. pick 2 basically, there is an opportunity cost