FWIW I think “Please don't complain that a submission is inappropriate. If a story is spam or off-topic, flag it.” is different from the others.

It’s an instruction for how to use the site. It’s helpful to have it in the guidelines for when the flag feature should be used. Without it, the flag link is much more ominous.

Maybe it could be consolidated with the flag-egregious-comments rule?

Edit to add: IMHO it is not at all obvious on this site that flagging stories is meant to be roughly the equivalent of downvoting comments (and that flagging comments doesn’t have a counterpart at the story level).