That's a stock phrase that I use to acknowledge that internet comments can land in all sorts of ways with readers, depending on their prior experiences and what's going on in the moment: https://hn.algolia.com/?dateRange=all&page=0&prefix=false&qu.... It doesn't imply that the GP comment was wrong or annoying—only that if it was, it's still not ok to break the site guidelines.

When I read your GP comment, though, I can see how some people would find it provocative, because it sort of follows an internet snark template: "<mild factual observation>, but <sudden putdown>". Not saying you intended it that way! But intent doesn't affect much, unfortunately. If your comment had stopped before the "but" clause, it would have been just fine.