Per my experience, you go to the Yamaha dealer's parts counter and have a choice. You can either ORDER the matching key from Yamaha or ORDER the key blank (Yamaha part no. 4BH-82511-09 for an '05).1 If you order the blank, the dealer won't cut it; you have to find someone who will.
It is a good deal more difficult to align the Yamaha blank and template key properly on the template/cutting machine than most keys. I got lucky and my local TruValue hardware store has someone2 who paid attention to detail, double checked that he had the right clamp installed and that he had aligned it all properly before cutting me a perfect key. I bought two blanks at the dealer but only had the hardware store cut one, so I have an extra that isn't cut. Why did I buy blanks instead of the pre-cut key that Yamaha could have provided instead (from the number on the tag)? Because the pre-cut key was something like $21, while the blanks were around $4 each. I think I paid about $2 to get the one cut.
Just reporting my experience when I lost one of my two '05 FJR keys. Sorry it doesn't make as much sense as your expected (also my expected) procedure.
1 Black end plastic thingee part included with either option when it comes in and you pick it up.
2 First key maker guy bailed after some trouble setting it up, and went to get the store expert.