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I had the same problem. I was using a single management server while the multitenancy was handled by a single Enterprise Manager. You need the highest edition of Veeam (Enterprise+) and you still get a very limited functionality for your tenants.
Eventually I ended up with VMcom Backup Appliance (https://vmcom.com). It is dead easy to use and has a strong multitenancy built-in. All you need to do is to create tenants within the application and then assign permissions for selected vSphere objects - VMs, folders, resource pools, etc. Each tenant can see and manage only the objects they have permissions for.
good input - thanks again.