User with Administrator role is added to a subscription in Subscriptions > example.com > Users.
Tools & Settings menu and some website options (for instance, Additional Apache directives and Additional nginx directives) are missing in Plesk interface for this user.
User that was added via Subscriptions > example.com > User has limited set of permissions and cannot view or manage Server settings. It is not the same as the Plesk administrator. See detailed information about user roles in Plesk in Administrator Guide
If it is needed to add an additional user with administrator privileges to Plesk, follow the steps below:
Go to Tools & Settings > Additional Administrator Accounts.
Click Create Account.
Specify administrator account properties.
Specify account login, password and email address.
Specify the name of additional administrator account user in the Contact name field.
Click OK to finish the creation of additional administrator account.
Note: additional administrator accounts have access to all subscriptions on a server.
See more details about additional administrator accounts in Plesk Administrator's Guide