Turns out the problem was even simpler — I had recently reinstalled Deluge and I assumed setting it to Server/Client mode instead of Classic mode would mean the daemon would keep using its own config as normal, but for some reason it was taking all of its settings from the server-side config EXCEPT its "watched folder" settings.
Seems bonkers that it would ignore the server's watched folder settings and override it with the client's, but good thing I took a look in that folder to see if Flexget was actually downloading the torrents! When I spotted that inconsistency and fixed it all those torrents from the past week or so added themselves to the client.
So TL;DR, my flexget config was fine the whole time (except when I put that "seen: local" bit in the wrong place) and the problem was just that Deluge is designed to work counter-intuitively.
Thanks for the suggestions all the same!