So this is why is more weird. SSAO & light shaft can handle even better with a custom version of UE3.
No, we can't say that these effects should be handled better because Gearbox has modified the engine. They modified the engine to handle what they need, such as larger environments and probably more enemies for example. That doesn't mean they optimized or modified anything relating to SSAO or light shafts, they may be using Epic's implementation for both of these effects.
Basically just because it's a custom version of UE3, that doesn't mean these effects should be easier to pull off.