This has not got anything to do with Square Enix to be fair, this is more an issue with Sony. PC lets you back up your settings with ease because of the way the PC works. With PS3 you have to use a couple of methods which anyone can do.

Playstation Plus. All user settings are backed up to the cloud, so you can restore whenever you like. With PS4 requiring PS+ for most online game (though thankfully not FFXIV), I expect more people to use this feature.

Too poor for PS+ or don't want to in principle? Use the PS3's inbuilt feature to back up your user settings to a flash drive.