Yeah, those "ticks" you see in the logistic requests missing entities are the placeholder ghosts. The placeholders are needed for blueprinting and deconstruction of unapproved ghosts to work properly, and unfortunately it seems they have to be "buildable entities" otherwise those tools won't be able to select them. This is why they show up as missing entities in the alerts.
My thinking is that it's useful enough to be able to blueprint and deconstruct unapproved ghosts to be worth the annoyance of having to see those tickmarks in the alerts. I'd like to find a better solution, but I'm not too optimistic about it at this point in time.