I don't think it's true that archive links are auto-flagged. I think [flagged] always indicates that it was flagged by a human: almost always a user, but occasionally a moderator.

Does anyone have evidence that would contradict this?

There are some things that are automatically [dead], though. Here's a post by Dan from earlier this year explaining some of the inner-workings: https://news.ycombinator.com/item?id=30273707