Deploying a LoRaWAN gateway running the Basics™ Station Semtech Packet Forward protocol as a balena.io application.

Ah, probably it’s because the USB2 interface is disabled by default on the CM4. You must add dtoverlay=dwc2,dr_mode=host to the config.txt file.
See Balena CM4 IO Board image: usb support - #6 by nmx
Can also be done from the dashboard under the device configuration option.