Well, if the FAQ says you pay everytime, then the rule is you pay everytime. If you want to houserule it that you only pay once, that fine -- but it's a house rule, not the regular rules.
You could think of it like a housecall fee. If the plumber charges $60 just to come to your house, and he fixes everything in 1 visit, you only pay the housecall fee once. If you have him fix everything over the course of 3 visits, then you have to pay 3 times - even though the end fix is exactly the same.
In the case of cold iron, I guess you could say it cost 2000gp to make it ready to accept magic. If you magic it all at once, you pay the fee once. If you want to magic it over the course of 3 times, then you pay the fee 3 times. If you want realism, then play something else
FWIW, I'm gonna play with the house rule that it's a one-time fee. Not that it matters, since nobody in my group has ever magicked cold iron.