I believe per TweetDeck documentation (https://support.twitter.com/articles/20170322) this is the difference:
filter:nativeretweets shows retweets from users who have hit the retweet button.filter:retweets shows old style retweets ("RT") + quoted tweets.
Those are filtering FOR those types of results, but as you've done, the - is necessary to filter them out -filter:nativeretweets or -filter:retweets