The patch itself is clearly a different file – but it appears the version number has not been updated.
Can’t reproduce this. I see the correct version number both when inspecting the app in the Finder, and also via the About Unity dialogue within the app.
Are you sure you’re running the right app?
Can you do:
terminal% grep 4.6.1 /Applications/Unity{blah}/Unity.app/Content/Info.plist
Where {blah} is whatever you might have used to name this install. I suspect this will say the application in 4.6.1p2 and not p3.