It seems like Apple hasn't really improved the pairing process on tvOS, but I have some tips for you.
Assuming that the USB-C remote is not paired to any Apple TV at the moment, unplug and plug in the Apple TV that you want to have paired with it. Do not touch the remote that's currently paired with that Apple TV. As soon as that Apple TV boots, press and hold the Menu (back) button and Volume up button at the same time, while holding the Remote less than a foot from the ATV box. Do this about 10 seconds. See if there is a prompt on the screen to finish the pairing process, or it may pair without a prompt.
If you are unable to pair the Apple TV remote, there could be a problem with the tvOS software or the firmware. For example, my Apple TV 4 (HD) doesn't behave the way it is supposed to, I always suspect that there is some bugs that lingered from past updates.