I do get a few packages to upgrade when I do as you suggested. Strangely enough none of them show in the Software Updater, despite it regularly displaying other updates:
Here’s the output of apt list --upgradable
after sudo apt update
Listing... Done
compiz/xenial-updates,xenial-updates 1:0.9.12.2+16.04.20160714-0ubuntu1 all [upgradable from: 1:0.9.12.2+16.04.20160526-0ubuntu1]
compiz-core/xenial-updates 1:0.9.12.2+16.04.20160714-0ubuntu1 amd64 [upgradable from: 1:0.9.12.2+16.04.20160526-0ubuntu1]
compiz-gnome/xenial-updates 1:0.9.12.2+16.04.20160714-0ubuntu1 amd64 [upgradable from: 1:0.9.12.2+16.04.20160526-0ubuntu1]
compiz-mate/xenial-updates 1:0.9.12.2+16.04.20160714-0ubuntu1 amd64 [upgradable from: 1:0.9.12.2+16.04.20160526-0ubuntu1]
compiz-plugins/xenial-updates 1:0.9.12.2+16.04.20160714-0ubuntu1 amd64 [upgradable from: 1:0.9.12.2+16.04.20160526-0ubuntu1]
compiz-plugins-default/xenial-updates 1:0.9.12.2+16.04.20160714-0ubuntu1 amd64 [upgradable from: 1:0.9.12.2+16.04.20160526-0ubuntu1]
gir1.2-unity-5.0/xenial-updates 7.1.4+16.04.20160701-0ubuntu1 amd64 [upgradable from: 7.1.4+15.10.20151002-0ubuntu2]
libcompizconfig0/xenial-updates 1:0.9.12.2+16.04.20160714-0ubuntu1 amd64 [upgradable from: 1:0.9.12.2+16.04.20160526-0ubuntu1]
libdecoration0/xenial-updates 1:0.9.12.2+16.04.20160714-0ubuntu1 amd64 [upgradable from: 1:0.9.12.2+16.04.20160526-0ubuntu1]
liblightdm-gobject-1-0/xenial-updates 1.18.2-0ubuntu2 amd64 [upgradable from: 1.18.2-0ubuntu1]
libunity-protocol-private0/xenial-updates 7.1.4+16.04.20160701-0ubuntu1 amd64 [upgradable from: 7.1.4+15.10.20151002-0ubuntu2]
libunity-scopes-json-def-desktop/xenial-updates,xenial-updates 7.1.4+16.04.20160701-0ubuntu1 all [upgradable from: 7.1.4+15.10.20151002-0ubuntu2]
libunity9/xenial-updates 7.1.4+16.04.20160701-0ubuntu1 amd64 [upgradable from: 7.1.4+15.10.20151002-0ubuntu2]
lightdm/xenial-updates 1.18.2-0ubuntu2 amd64 [upgradable from: 1.18.2-0ubuntu1]
linux-firmware/xenial-updates,xenial-updates 1.157.3 all [upgradable from: 1.157.2]
python3-distupgrade/xenial-updates,xenial-updates 1:16.04.15 all [upgradable from: 1:16.04.14]
python3-software-properties/xenial-updates,xenial-updates 0.96.20.3 all [upgradable from: 0.96.20.2]
software-properties-common/xenial-updates,xenial-updates 0.96.20.3 all [upgradable from: 0.96.20.2]
software-properties-gtk/xenial-updates,xenial-updates 0.96.20.3 all [upgradable from: 0.96.20.2]
ubuntu-release-upgrader-core/xenial-updates,xenial-updates 1:16.04.15 all [upgradable from: 1:16.04.14]
ubuntu-release-upgrader-gtk/xenial-updates,xenial-updates 1:16.04.15 all [upgradable from: 1:16.04.14]
I’ve seen all of these for a while on Synaptic. I just never update from it, only from what the Software Updater tells me to. But in any case Libre Office doesn’t show here either.