I've answered my own questions:
If you make a faction, the metal color changes the metal for the entire faction.
If you just a sovereign, the metal color only changes the weapons the sovereign holds.
I do like that effect, but I hope that the manual or a tool-tip will tell people that changes to the metal color on the sovereign only effect the sovereign. Maybe have this written on one of those spiffy load screens with tips about the game.
This doesn't address that all weapons do not change with metal color. Is there a reason for this or just an oversight?