To anyone else who might have this issue, here's a permanent work
around.

Open a terminal and edit console-setup config to manually input the
thinkpad variant.

gksu /etc/default/console-setup

and look for a line that reads

XKBVARIANT=""

and change it to

XKBVARIANT="thinkpad"

After that, a logout should suffice for X11, if not, restart hal.

For console,

sudo dpkg-reconfigure console-setup

would do the job, in theory, but since it's missing the variant this
will either overwrite the manual change, or present a TUI menu to
configure the layout, showing the same options that Gnome's (and KDE's?)
GUI show.

It appears this bug is indeed about the specific information not
existing in a central location (package xkb-data?), AUIU.

-- 
abnt2 keyboard layout missing thinkpad variant
https://bugs.launchpad.net/bugs/359719
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