I think that it's the same thing, but it saves you a step.
It's been so long since I've not been jailbroken that I never really have any reason to restore from a backup. I keep them around, in case I need them in an emergency, but I always go from one jailbroken device to another.
Before I update, I save my camera roll to my computer. Then I use "DataDeposit" from Cydia to back up any data from App Store apps to DropBox. To be perfectly honest, there aren't a lot of apps that need backing up, mostly games and the occasional odd app that doesn't store the data somewhere in the cloud. I usually don't care about Messages backups.
I restore the phone as new, then enter my iCloud ID when going through the setup screens. After I Jailbreak the phone again, I just install DataDeposit again to restore any App Store data when I reinstall an app has backed up data. Sometimes they don't get reinstalled for a long time, so it's like spring cleaning.
If you've got a lot of email accounts or VPN settings, you should check out the iPhone Configuration Utility. You can set everything up on your computer with its real keyboard, then push it all onto your phone. Makes setting up a new phone rather painless.