It’s to prevent the user error when user will set some clearnet net qube e.g. sys-firewall instead of sys-whonix as anon-whonix net qube.
There are links to reddit and Whonix forum in the github issue that shows the issue:
When you use Whonix Workstation you expect all traffic to go through Tor without any clearnet leak, but if you set Whonix Workstation net qube to be a clearnet net qube instead of sys-whonix then it could lead to a leak through clearnet.