Hi,
I think that if you need to use NC, you should find a way to NOT use infrastructure mode. It would really change the network behaviour, and the results would be completely different from the ones you expect.
In order to build a butterfly topology with ad-hoc nodes you need a routing protocol (to be on top of NC, more later) and a precise node positioning, in order to build a logical topology out of a physical one.
About the routing, it really depends on what is your NC algorithm. This is often neglected in the papers, and most of them assumes that a source wants to send packets to ALL the nodes in the network. This can be accomplished with a controlled flooding algorithm. Alas, controlled flooding isn't implemented in ns-3. You could develop it tho, it shouldn't be too hard: take any ad-hoc routing protocol, trash everything in it (all) and just add a function to not forward packets if they have been recently forwarded. You'll need to find a way to recognize if a packet has been recently seen, but this is not dramatic.
About ARP and APs, I can ensure you that packets flow through the AP in all the infrastructure mode examples. Just check if the packets are "doubled" (sent twice by two different MAC addresses). Moreover, double check the MAC addresses, and remember that 802.11 MAC header doesn't have just two addresses, it does have up to four...
Have fun,
T.