I looked into this and I can reproduce it too.

The reason is that in the target filesystem there is no "restricted"
packages list anymore (because that is removed from the sources.list in
target). So when apt tries to figure out the section it can not find a
Packages file and falls back to /var/lib/dpkg/status. That has "base".
This comes directly from the deb package that has "base" too instead of
"restricted/base".

To fix we need to add "Section: restricted/base" to the deb or gather
the information what is restricted and needs to be removed before
removing "restricted" from the sources.list (plus we need to have
indexfiles that match the current mirror in sources.list - it seems like
this is not always the case on the /target filesystem).

-- 
"only free software" option installs linux-restricted-modules
https://bugs.launchpad.net/bugs/290925
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