I've got at least another board with unplated copper,


(Note, second pic is at a right angle to the first; note the bigger and smaller empty holes, and the common hole with a brass insert.)
This is a HP/Compaq 8510W motherboard; this area is between the Northbridge and Super IO chips.
I would assume they used a somewhat more reactive flux in the solder paste, relative to the recommended low activity flux, RoHS paste and gold plated boards, that are most common for assemblies.
The copper parts look coppery, but remember, a bright copper surface is... well, *bright*! Almost as bright as the brass. So there's more than a few years of tarnish on there (almost five, in this case, actually).
Tim