I don't know much about metalizing on faying surfaces, but I do know something about paint, and "no paint" is probably exactly right if those are slip-critical connections. Your client needs to be able to provide the information about whether the bolted connections are slip-critical and, if so, what class they assumed in the design. Almost surely the paint can't provide the required slip resistance; topcoats typically don't. (For the metallizing, it's probably as good as a roughened galvanized surface, Class C (similar to Class A), but I don't know that for a fact.) They'll have to find a way to get those connection areas painted in the field.
If they're shear/bearing (non-slip-critical) connections, then painting the whole thing is probably fine.
There's a lot of good information in the RCSC Bolt Spec:
http://boltcouncil.org/files/2004RCSCSpecification.pdfHg