Airport extreme seems to place a limit on gigabit ethernet
After hours of pulling my hair out I'm going to answer my own.

TL; DR: Airport Extreme (at least the 2013 edition which I own) is crap for gigabit networks.

It's advertised gigabit ports cannot go over, after much testing, 205mb/s because of the WAN to LAN routing which is horrible.

This is a decent wireless router but overpriced for what it offers in terms of range and Ethernet performance. If you buy a gigabit internet do not make the mistake and buy it because it can't go faster than those 200mb/s.

As I said, after much reading and testing, your best bet is with a device that has hardware routing and I strongly recommend you take a look at this page for comparisons of various devices in terms of "WAN to LAN Throughput".

I just ordered a ASUS RT-AC87U which seems to offer a great signal and solve my gigabit issues. I will update this answer once I receive it and manage to do some testing.