What is the goal here? There is no reason to install Wireless package on 802.11ax device, it can be done, but then indeed to local radios on it will be lost.
BaseBox2 using Wireless package can connect to cAP ax, which uses wifi-qcom package.
BaseBox2 should use wireless package, and cAP ax, should use wifi-qcom package.
If you uninstall the mentioned packages on one of the devices, that device will lose internal radio. By default there is no need to do anything with the packages, devices will work out of the box.