If you have less than 5000 total endpoints, then don’t worry about things like this too much. Even if they all selected the root, you’d probably be fine, even though it isn’t ideal.
You can have the Root server advertise a Relay Affiliation Group of ROOT and have no clients use that affiliation group. This will prevent the root from being selected during Automatic Relay selection of group * by the clients, but it will not prevent the clients from using the root as a last resort, which is generally what you want.
You can set up a fake root relay, and it will handle the clients that failover to the root.
You can use relay weight and priority to influence which relays are selected during automatic relay selection of a particular group.
I haven’t tried this, but I would recommend setting up a failover relay that uses port 443 instead of 52311 and set that as the failover relay on all clients. The clients will only attempt the failover relay before they try the root as a last resort.