Promoting a clarification from comments: we only have two choices with comment flags, delete the comment or decline the flag. There's no "helpful but no action" option like with post flags. Declining the flag doesn't mean there's no merit whatsoever, it just means we didn't delete the comment.
While it's definitely not good for comments like that to dominate, I don't think it's an issue to have one or two now and then. A little bit of friendly human interaction can make the site a little warmer for people. I'll generally delete things like that if there's multiple, or if the question is older; there is indeed a good reason it's technically against the rules. It's just a spot where a teensy technical violation of the rules seems to me to not cause the problem the rules are meant to prevent, so I'm fine being a bit flexible.
To be clear: we definitely do delete off-topic conversations, comments that invite chatting, old side notes that people gave the OP that are no longer relevant, and all kinds of other things. I'm not saying anything goes. I'm just also aware that there's plenty of history of "welcome to the site" comments and similar, going back before I was a mod, with no sign of problematic consequences, and plenty of positive effects in encouragement of question authors, and I'm not inclined to forcefully change that without strong direction from the community.
And for what it's worth, I've seen this on other sites too, not just here, especially with "welcome to [site]" comments - one encouraging comment is fine, probably even good. It's when it turns into piling on, or a conversation, that it crowds out useful comments.