Hi,
I don't know what the goals of the paper are, but the different implementation may lead to completely different results.
As an example, AP in ns-3 can link the wireless and wired ports through L3 (the normal behavior) or L2 (by using the Bridge NetDevice).
However, the result will be always slightly different than what you can have by using two switches and one OpenFlow controller.
There's a new OpenFlow implementation for ns-3 (it has been announced in this list, search for it). Maybe it supports your configuration. Try asking its dev.
Cheers,
T.