I'd argue that flagging paywalled pages is based on content and not provenance. If I follow a link and can't read the article then there is effectively zero content.
That's a good point and I agree. But the standard workarounds mean that the content is available. It's an annoyance to have to follow two links instead of one, or open a different window. But the cost/benefit of sacrificing good content to avoid that annoyance would be way off for HN.