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At a quick glance, that list has mistakes in it.
For example, it lists 愛憎 (あいぞう, likes and dislikes) as あいにく (unfortunately, regrettably), which is also the common word that you should be learning.
Even if you had an automation tool, you would have to check every word anyways.
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You can export your anki deck as .txt file. Then you could compare the 'expression' columns of your deck with the N1 one automatically and generate the 'missing' cards.
However, as you hinted, I don't think it'll be worth the hassle. When your vocabulary is still very limited, vocab lists are useful in order to get you up to speed quickly. However, once you have a solid basis the vocab you encounter and that would be useful to know heavily depends on your interests. Therefore, a one-size-fits-all vocab list just can't be made anymore.
With regards to the JLPT, I'd continue reading and adding unknown words you deem useful to anki. If I remember correctly, there's no official N1 vocab list anymore and the makers of the test don't want you to just blindly memorize the required vocab and nothing more. I think they even had some clause like '10% of the words in the reading section can be unknown/difficult/etc and is at the discretion of the test makers'.
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Good luck! I used the tanos N1 deck to study when I took (and passed) N1 last December. I took each word and added a sentence with it from the Green Goddess Kenkyuusha dic, or Daijisen. Then I added definitions from monolingual dictionaries and/or Kenkyuusha to the back of cards as necessary. One thing I noticed about that deck was that it only gave the kana for a lot of words which would have their kanji show up in the Vocabulary section. I added the kanji to all of those, as long as Daijisen or Koujien didn't mark the kanji as rare.
On one hand reading novels helps a lot. A lot of the words which were on the test but not on the vocabulary list I knew from reading novels. On the other hand, the test I took seemed to rely a lot on the words in the tanos list too. It might be good to at least skim it and add unknown words to your deck.
Edited: 2014-07-01, 12:34 pm
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Keep in mind that there is no word list since they moved to the N5-N1 system they use now. The old test specification when it was 4級 up to 1級 used vocab lists, but the new test specification basically just says, "eh, the vocab is whatever we feel like putting on the test..."
So those lists you see up around the web and in Anki decks are probably useful as a guide since they came from the word lists in the old test spec, but they're probably not exhaustive in the way you might be thinking they are.
So be careful, and practice reading from real native sources. Newspaper editorials and magazine articles are especially useful for studying for the JLPT. This will give you the opportunity to learn some of the new vocabulary that might be on the modern test.
Edited: 2014-07-01, 11:50 pm