pkg autoremove doesn't do what you think it does.
pkg autoremove is used for removing orphan packages, which were installed
during dependency resolution and are no longer needed.
What you should do is pkg delete <pkg> for what you want to uninstall. Then there are a number of steps needed to install a port if you are going to use make.
First step ...
What you see on bugs is conversation regarding updating to unifi6. It's not available in ports right now but, since the PR was only filed six days ago, it looks like someone is very, very close to completing it.
In the meantime, it's not available anywhere from FreeBSD itself. The best you could do right now is try to install it yourself from the unifi site ...