The Alliance Y-Wings are mostly altered to have the turret removed, as well as most of the armor, to make them faster, a little more maneuverable, and more reliant on the on-board astromech to help in ship operations. The turret is replaced with a fixed-front dual Ion Cannon then, but it can be fixed to face dead 0 in the rear as well (though that's only mentioned, never actually seen in games or anything).
Some Y-Wings are altered then in EU, as originally in the EU the ion cannon was what the ship came with just like in the OT, however the Y-Wings in their original state now (as we see it in Clone Wars 3D) has a different turreted rear gunner... The EU Y-Wings with dual seat cockpits have the rear-gunner sitting similar to the Snowspeeder pilot/gunner duo, and he is able to operate the ion cannon on top rotating it 360 degrees + tilting up/down somewhat.
So, the summary of all that BS is that there's the Clone Wars Y-Wing which is a YW in its original state. There is the original trilogy Y-Wings then, with their heavily stripped down looks, and removed gunner turret with a fixed forward ion cannon mounted on the cockpit top. Then there is the EU Y-Wing where either it's an alteration the Alliance has made, or Y-Wings were maybe produced with this alteration as well, where there's a back-to-back configuration for pilot/gunner, and there's a movable gun atop the craft for the gunner to fire.
The CW3D Y-Wings have goofed up the EU continuity somewhat with the YW, but at the same time they're adhering to the YW being an old craft that dates from the Clone Wars. I would've liked seeing Z-95's myself.