Sorry i'm a little confused.
When you login with Domain account you do not see SSO and Discovery but you see the inventory?
But when you login with admin@system-domain you see the SSO and Discovery but you don't see the inventory?
That sounds perfectly fine to me.
The domain account is the administrator account who can see the inventory.
The SSO admin(admin@system-domain) is the account that sees Configuration under SSo and Discovery.
Just verified with my environment. That's exactly how it should be.