Here is my analysis:

apt-get, etc. uses the environment variables, unless apt.conf overrides
them. Using gnome-network-properties, only the proxy is stored in
apt.conf, without the exceptions. Automatic proxies are not stored at
all.

Synaptic, etc. does not pass proxy settings (the sudo call does not
preserve the environment), and so wget does not know about the proxy and
tries to connect directly.

Without the apt.conf, when sudo suing and setting environment variables,
apt-get works correctly for all cases.

-- 
gnome-network-properties does not set apt proxy correctly
https://bugs.launchpad.net/bugs/631185
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