The margin indicator is intended to be a convenience feature - it provides an at-a-glance indication of information already accessible from each post's moderator menu. Placing it in the margin ensures that it doesn't interfere with anything else on the page, because nothing important goes in the margin.
Of course, if the browser window is narrow enough that margins aren't displayed, then there's no room for it. No matter; the mod menu retains this same information.
I suppose it could be hidden entirely when the margins don't allow room, but I would rather see it even partially clipped than risk missing it if I happen to use an insufficiently-wide window. This is a fairly utilitarian feature - retaining full utility even at the expense of appearance is important, else it might as well not exist at all.