Newbs and insecure people find the motherboard manual great because it tells you everything you need to know about building a pc. I'd not reccomend someone who has not put together multiple pcs go forth without one.
Nearly all motherboard manuals are available online in .pdf format. So the manual is fine, but you aren't guaranteed any screws, standoffs, cables etc. That's the worry I have about open box mobos.
Usually you get everything with the Open Box stuff, idk why Newegg tells you that you would not get it... unless the lazy person didn't put the stuff back you get everything like as if it was new