Your Safari update *may* have been released as part of an incremental OS X update (as has happened in the past), thus, no freestanding update. (Does MacUpdate actually offer a Safari 6.1.2 d/l? I couldn't find it.)
There have been updates prior to the Mac App Store Update that have also not been available other than through SU, Java, I believe, having been several of them, but I've never been certain as to why.
I wouldn't trust a source other than Apple for Apple d/l's.