The cct V0.5b shows an option of connecting the Xbee to the LiIon V_bat – which can get to 4.2V – and a very nice low impedance for the Cellular Tx power requirements.
So if the Xbee-V1-UT/XB3-C-A2 Cellular @ 4.2V was pulling up, that would over drive the mega1284 pins above their Vcc (3.3V).
At some point the megas1284 protection diodes start to conduct. The issue not stated in the Xbee docs is if there is a -RESET pullup. If there is no pull-up, or its week (greater than 100K) its probably workable.