Is it legal? Isn't injecting stuff into other people's websites protected in some way?
It's a nasty precedent. One stop of browsers banning you from access to competitors websites.
I think the only legal issues is from an anti-competetive angle which the courts would have to settle. I don't think they are violating any sort of computer crime laws. It definitely feels slimy, though.
Net neutrality? Trademark infringement?
Worst case scenario, they could just move the banner to be "within the browser's GUI" (while still seeming to extend over the page) rather than actually in the page and that issue would go away.
I think it's already this way right now. Look at the scrollbar height on the screenshot in the article.
I would imagine the antitrust judgement would have given them pause in implementing something like this but here we are...
Listening in to what users do is the way to earn their trust and if they don't get it by themselves what could be better than telling them straight away.