The FSF post didn't say either what terms of the license they thought Apple was violating, nor why they think distributing via the app store is any different than distributing via the post office.
If I mail GPL software via the postal service, I have to comply with the GPL, which mainly means I have to include an offer to provide source code upon request. The postal service doesn't have to do ANYTHING regarding the license, they are a third party facilitating my distribution. It could be argued that Apple is no different- the person distributing via the app store needs to comply, Apple doesn't have to do anything to be in compliance.
By the wording of the license, it would be possible to argue either way, so a court would look at the INTENT of the license, it's PURPOSE. The gpl helpfully states it's purpose and intent right at the top - to maintain the four freedoms. As long as the freedoms are being maintained (by having source available, etc.), the court would probably rule that it's perfectly okay to distribute via the mail, ftp, email, http, or the app store.