Linking to /newest appears to many HN users to just be a way around directly linking to their article.

I don't know enough about the voting manipulation detection implementation on HN, but I'd imagine a bunch of accounts hitting a direct link to an article and upvoting it could potentially be more suspicious than having them all click the article from /newest or just upvote from there.

FWIW as an anecdote, I've seen HN voting manipulation kick in quite hard when people link directly to submissions.