Hi and welcome to the commmunity!
We could potentially use Veeam Endpoint Backup FREE to protect the VM
Could you please clarify which VM are you going to protect with Agent for Windows? Or did you mean to say "physical machine" instead?
In this scenario, should I install this on the Veeam backup and replication physical server and then backup the server on to a Cluster shared volume on DR HyperV cluster
You can do that. In order to restore VBR server you'll have to use Recovery Media and perform a BMR either into a new VM, or into a physical machine. There are two more ways to protect VBR server for DR:
1. Use configuration backup
2. Place production VBR server on the DR site so if any thing happens with production site, backup server will be on DR ready to initiate DR activities