If XCTU doesn’t recognize the XBee3, that’s a pretty bad sign. How are you attaching your XBee to the computer? Do you have the USB-C XBee3 carrier? https://www.digi.com/products/models/xbib-cu-th That development board should make sure the bee is awake and work flawlessly with XCTU. Are you plugged into the USB-C port, not the side microUSB? Is the other end of the USB-C that’s attached to your computer attached to a USB-3 power delivery port?
If you’re using another carrier/development board (ie, not a Digi one) it’s possible that the bee is asleep or not sufficiently powered and that’s why it’s not talking to your computer. Make sure whatever carrier board you’re using has pin 9 on the bee socket held at ground to keep the bee awake for communication and provides up to 1 amp power. A “standard” USB port will only provide 500mA power, which is NOT sufficient for the LTE XBee3 and may cause it to brown out. An unmodified Mayfly will NOT work as a carrier board for your bee to talk to the computer
The u-blox M-Center program is not likely to recognize the chip on the XBee unless you have both programmed the XBee to be in USB direct mode and connected the USB direct pins to your computer. I don’t think there’s anything you can do with the m-center program that you can’t do with XCTU, so I wouldn’t bother with it if you don’t need to.