The packages being held back when you use apt-get update are new packages that are going to be installed. So I suppose you could that they aren't strictly speaking updates.
To install all the updates from the command line and have nothing held back, use
sudo apt-get dist-upgrade
Contrary to what you might think, the first one doesn't take you to the next Ubuntu version.
sudo apt-get dselect-upgrade
So, presumably update-manager is actually doing apt-get dist-upgrade in the background.