The update is slightly different for each device. The update for the phone addressed that issue with being able to bypass the Passcode on the phone and that issue did not exist on the iPad - or at least it was never reported.
Are you using iTunes to download the update? You still have to install the update on both devices no matter how you do it. You cannot "sync" the download to all of your iOS devices and do it all at once using only one download on one device ....if that is what you mean.
So even though they have the same iOS version number, 6.1.3, they are actually different. If I were King of Apple, I'm not sure that's how I'd do the version system.
Demo, I know have to to update them both. That's why I noticed this issue, I had downloaded the update for my iPhone 5. And it updated perfectly fine. Then I went to update my iPad 4, and it started downloading the iOS update. I thought possibly I had done something wrong. Apparently, it's normal.
Still, a universal update would be much easier. I'm sure the Apple coders are smart enough to write code that would install the right code to the right device. We used to get Universal OSX updates that knew if you had a G5 or Intel Mac.
Anyways, I guess I'm doing it right. Cool.