Assuming you read through the security section of the documentation.
You could create a user role for each module access you require. System_User_View, System_User_Edit, etc. and link each one to the specific Module Role that only has specific access to certain entities. Your screenshot above would be an alternative way to assign user roles to the individual users.
Setting up the access to pages, microflows etc automatically affects the navigation. A short explanation on that topic can be found in this section of the Rapid Developer Course.
Hope this helps