Heh, heh. That would never have happened with Gary and co. hand-stapling them.

Nope; definitely never seen that before.
Nice to have in that context, IMO.

Does say something about the printing process, but wouldn't be impossible to fake. (Certainly not one to buy via eBay with the usual low-res scan, unable to take even a casual glance at the staples).

Generally printing flaws & defects do not increase the value of an item significantly.  This happens quite often during the process of producing printed media, whether it is automated or done by hand.  With rare items it can make them more valuable, simply because they are an anomally.  I would suggest that they can actually have a negative effect too if the items graphics or text are illegible or partially eliminated due to the flaw/defect.

With respect to the Men and Magic book.  At the very least it protected the inner cover and kept it in better condition.  But as far as increasing the value, I would suggest not.  Never know though.  Sometimes collectors go for unique copies!  I have always been interested in them personally.