Why not simply only suggest the packages for removing which "sudo apt-
get autoremove" would remove? It never suggested for me to remove any
manufacturer-supplied printer drivers or other third-party packages.

Your suggestion to whitelist the packages which are installed without
using apt does not help for printer drivers auto-installed with Jockey,
as these get also installed via apt.

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https://bugs.launchpad.net/bugs/458872

Title:
  Don't mark for removal manually installed packages

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