To truly bypass the Digi processor and communicate with the u-blox module directly, you'll need to configure the XBee3 modem in the USB Direct mode:
https://www.digi.com/resources/documentation/Digidocs/90002258/#concepts/c_mode_usb_direct_lte-m.htm?TocPath=Modes%257CUSB%2520direct%2520mode%257C_____0
We had to use this mode to conduct FCC compliance testing on our hardware - The other end of the USB cable connects to a PC that runs the u-blox m-center software in order to drive RF testing commands.
For normal application, we have a Microchip PIC32 chip as the host processor running XBee ANSI Library:
https://github.com/digidotcom/xbee_ansic_library
I don't know why you need to communicate with the u-blox module directly. The beauty of using a XBee modem is that the cellular and Internet connection are all handled by the modem itself.