Q1 will this topology reduce or better remove transmission conflicts?
No, simply enabling the Coordinator function will not keep you from receiving data from unwanted nodes or networks. You must set the Channel, PAN ID or both functions to keep from receiving data from unwanted networks.
Q2 some end devices are low powered and use the DTR to sleep the Xbee, will the Xbee handle being told to sleep while still having to wait on the coordinator?
If you are going to use the sleep functions, it is better to use the cyclic sleep with Pin wake or use the Cyclic sleep function and have your processor monitor /CTS. When the module is awake (ST), the CTS line is active Low and you can send and receive data. When the ST time expires, the CTS line changes states and the module finishes its current request and cycles to a sleep state.
Q3 will the end devices need any settings to be changed to allow them to associate?
If you are going to use the Association functions, they yes you do need to set the A1 and A2 functions accordingly on both the Coordinator and End device.
Q4 can i go back to a peer to peer by stopping the main receiver being a coordinator CE0?
Once you enable the Association functions, you really simply can't turn off the CE command on the Coordinator and still expect to communicate with the your end devices. Now if you do not use the Association functions, then yes you can.