The solution that worked for me was emptying /etc/apt/trusted.gpg.d,
running apt-get update, and then manually adding every key it blocked on
to the main /etc/apt/trusted.gpg keyring with apt-key adv as described
above. Nothing else turned out to be necessary, you can leave the
/etc/apt/sources.list.d/* where they are. There's probably a smoother
way to consolidate all the keyrings in /etc/apt/trusted.gpg.d/* into the
main one using gpg itself, however, that was quicker than writing a
script.

I really shouldn't have to do this in the first place.

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https://bugs.launchpad.net/bugs/1263540

Title:
  Apt-get reports NO_PUBKEY gpg error for keys that are present in
  trusted.gpg.

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