It is entirely reasonable that a site which displays different content to what was shown at time of submission, purposefully because of HN, gets flagged.
As for the flagging, the guidelines say otherwise. A change in leadership and governance of a prominent open source project is noteworthy to the point that discussion on HackerNews is a perfect fit.
Right here, of all places, people should be able to either understand the banner, or ignore it and get to the point of the article.