As others have chimed in, your dealer is wrong. The spare key fob will work with the 08/09.
Thing is, most Kawie dealers so seldom deal with Concours and especially the KiPass system, that the techs have little practical experience.
Like you, I bought a "used" (822 miles
) model and only got the one big fob. Also paranoid like you, I bought a spare key fob, went down to the local K shop and then watched them spend 3+ hours trying to program it. Didn't succeed and I left. They didn't charge me for the time because they honestly couldn't figure out why the damn thing wouldn't accept the program code, but told me they'd nag Mama Kawie until they figured it out.
Three weeks later I came back at their request and with 3 more spare key fobs I'd bought and they had 2 of the 3 programmed and the bike buttoned up in 15 minutes! The difference was that their tech guy had talked to the right tech guy at Kawie, learned the procedure AND that I had multiple spares. Turns out the first one I'd brought in was DOA, hence it couldn't be programmed. I got a refund on that one. This might also be what you encountered.
Try a different dealer and get a couple of additional credit card fobs and take them all with you.