So you want the programmable XBee module to work as a standard XBee radio by automatically going into "Bypass" mode that you currently put the module into manually?
Simple, write a program on the XBee to do just that. The use case you describe is included in the XBee SDK as a demo app (XBee/Serial Bypass).
1. Compile the example program included in the XBee SDK in CodeWarrior.
2. Upload the application to the programmable XBee via XModem.
2.1 You can use either the legacy-XCTU program to do the transfer or
2.2 You can try out the tool I wrote for easy flashing of the Programmable XBee (tested only in mac/linux atm): https://github.com/exsilium/pxbee-fwup.js
According to Digi, this method adds approx 0.9uS of jitter as everything gets passed via the HCS08 processor prior to reaching the radio chip.