This may come across controversial and i'm not meaning to sound that way however;
Take the cost out of it, it is an old car, obviously as with anything it's guess work a lot of the time when importing. It's something that can easily be missed..
I suspect quite a few cars on here have un-recorded little shunts in their histories that the owners probably don't even know about - it's only after taking alot of stuff apart you might see the signs. Yours is potentially in a more visible area (if that's what it is). Even the Auction graders can't always be 100% accurate, they usually go by obvious signs, or whether a car has gone through auction before having had obvious accident damage. In which case it is still subjective.
The place where you have an issue with is not somewhere that i personally would look to find any problems. (i.e. when buying a car, i wouldn't really think to check that part) maybe that's just me.
Try not to focus on that too much. You have a very clean, late facelift model with good mileage in stock form. If you want, i'm sure somewhere could strip that back, blend and spray it so it looks a bit cleaner. I would check mine for you but it's in a bubble at the moment and quite a faff to get open.
They are getting to the age now where they do need some attention and will never truly be like a brand new car.
I know what the dealer is talking about, in certain places the car does have flexible seam sealant but i don't think this is that. Perhaps they are getting confused.
If it helps, there is a website called carvx.jp - you put in your VIN and it costs about £13 and they send you a kind of history on your car, it shows previous times it went through the auction, as well as pictures sometimes if it has been involved in a shunt. I have used it multiple times, and it is well worth the money.