The legal entity of FAF (details here) doesn't own any copyright or trademark regarding Supreme Commander or Forged Alliance. We also do not have an explicit permission of the current rights holder Square Enix, however GPG explicitely mentioned FAF as a replacement before shutting down GPGnet.
So basically FAF operates in a grey area of the law. To protect ourselves, we decided to make sure that each user of FAF owns a valid licence of Forged Alliance.
As of now, the only way to technically verify that each user owns a Forged Alliance copy is by looking up your Steam or gog.com accounts game list, which is what happens during the account linking process.