It was recommended that you restore via itunes because restoring OTA or itunes gives different SHSH blobs from iTunes servers. This means that you would not be able to restore to 6.1 once apple stops signing 6.1. We have seen this in the past with 5.1.1 and 5.0.1, but this hinges on if the jailbreak team ever develops a tool for us to do SHSH restores.
So if you mess up you system after 6.1.x, then you would not be able to restore and you are forced to upgrade to a non-jailbreakable iOS.