Users flag stories, not the mods. If you have enough points, you van "vouch" for a comment. I don't know if it works at the story level. I don't see that option at least.

I seem to remember being able to vouch for stories. Maybe the karma limits have changed? Or it is also very possible I only remember being able to vouch for comments and confusing the two.

You can only vouch if the story is flagged and dead

Probably wants to avoid incendiary content (that attracts low quality discourse)

It is usually user-based flagging. There is nothing rational about that. I've been in both (flagging/flagged) situations.