If you believe the question is off-topic here, just vote to close. If you believe it should be migrated to another site, vote to migrate. No need to leave those comments.
You seem to be experienced in both Stack Overflow and the site's you are advising to re post in, but most comments I've seen of this type come from users who are not as experienced, and are very often misguided in many ways.
And leaving this commentshaving these comments laying around simply encourage other users to leave more of the same.
In any case, comments exist to "ask for clarification and add more information". These comments are most often deleted as "no longer needed", since they are not doing either.
Mods are not going to check the tags a question has, or when has the comment been posted and what's the 'last-seen' status for the user receiving the comment, nor how many close votes the question has or has not when reviewing "no longer needed" flags. These comments will be flagged, and generally flags will be honoured.
They are not rude or unkind, so there is no penalty. But best to accept their ephemeral nature.
It's not "wrong" to leave them, but you should accept that many of these are going to be deleted soonish anyway. More often than not the target for the comment had time to read them before deletion, so they are really no longer needed.
And if they are not paying attention to comments after posting their question, and the comments get deleted before they have a chance to read them... well, in all likelihood there weren't all that engaged in getting help anyway.