Wait, please remember the whole point of this product and your design is the KISS approach to complicated matters
Please do not change much in this free edition of the product - especially no web management interface!!!.
It should only be locally managed like today - maybe with an easy option to deploy agents and configs via AD policy.
What you should do is make 2 feature licenses to VBR called respectively "Managed ENDPOINT BACKUP" and "Managed PHYSICAL SERVER BACKUP".
The License "Managed PHYSICAL SERVER BACKUP" should add the following to VBR:
A new Navigation point called "PHYSICAL Machines" where you can do much the same as under virtual machines today - namely add managed servers, create jobs and restores.
When adding a server you essentially deploy a headless agent to a server (No localSQL, no user interface) and you should be able to do so by wizard, by AD policy or complete manually by downloading installer.
This agent just sits idle on the physical server waiting to be contacted and instructed to do backup. It should use/be a veeam proxy component like the virtual solution does today so all servers in the same job is Dedup'ed, compressed and shipped to a repository. Scheduling should be exactly the same as virtual machines - maybe called Physical Backup?. The same copyjob, tapejob and so forth should be possible.
The License "Managed ENDPOINT BACKUP" should add the following to VBR:
A new Navigation point called "ENDPOINTS" where you can do much the same as under virtual machines today - namely add endpoints, create jobs and do restores/Create recovery boot ISO's.
When adding an ENDPOINT you essentially deploy a small agent to a machine with No localSQL but a small GUI to restore and initiate a manual backup (if allowed).
Adding endpoints should be done by wizard, by AD policy or completly manually by downloading installer.
This agent is designed to get its next backup job config from the VBR server. It uses a configurable polling timer to request scheduling updates from the server. Prior to attempt polling or backup it does a DNS lookup for a special DNS name. If that name is available it start polling or doing backup if scheduled (or overdue).
Everytime it completes a backup it automatically gets its next backup schedule. The agent only ever knows about the next backup it should complete.
This agent should use destination infrastructure just like you do today in the free edition. Scheduling and destination setup is done centrally at the VBR console.
As far as I can tell these features should not require to much development as it uses technology, modules and features you have today. This would make VBR the ultimate backup solution in my book and still honour the KISS koncept.