We have different working environments: development, test, production, … 

The Visual Guard .Net Console allows you to create, see and manage several repositories at the same time in a tree view.
You can create one repository per environment.

Could we define different permissions set for different repositories?

Definitely. Permissions sets are created and managed in the Visual Guard Win console per applications. A permission set is created for an application. You can manage several applications in a repository.

Visual Guard .NET