In the case of "just" a link staying active, the problem might be simpler
to "solve": with a good BIOS there would be an option to enable or disable
wake on lan. Though most newer devices seem to come with terribly crippled
versions. So another option is to use "sudo ethtool -s eth0 wol d" to
disable it before shutdown. Should be sort of simple to automate that if
successful.
Other parts of the hardware might be left powered on without knowledge of
the chipsets which is likely NDA.

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Toshiba laptop battery is drained while shut down
https://bugs.launchpad.net/bugs/110784
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