As an ex-BMW dealer tech and a current main dealer tech elsewhere, I can tell you that this is VERY COMMON. In a busy dealership where bikes are just job numbers, no one really cares about your bike. It maybe your pride and joy, but in their eyes, it's just another bike coming through. A bit like a Hermes parcel.
Bikes get damaged ALL THE TIME. And no one wants to take responsibilty for it. This varies from dealer to dealer, the cost of the damage and their policy of "who pays for fuck-ups" In your case, they would have to replace the engine cases. It would cost a FORTUNE !! So no way is anyone owning up that one. From the driver to the manager.
The things I've seen hidden and damage un-reported would make you shudder.
My guess is that it's van damage. From the hooks, buckles or clasps on whatever strapping system they use. They've probably used your engine bars and the buckle has been flapping around. The paint is REALLY THIN. You really should have looked it over thoroughly after delivery but isn't hindsight wonderful.
OR. It's gravel rash or stone chip. Kicked up from the front wheel. (Did they test ride it?)
The bike hasn't been worked on (as far as you know), so I can't see how it would be tooling marks. But you never know what goes on behind those dealership doors when customers aren't looking.
I HATE MAIN dealers. Especially BMW ones. Having worked in them for so long. They're all coniving, dis-honest and obsessed about the bottom line over everything else. They might look impressive with all their clean glass, livery and frothy coffees. But behind the scenes are a lot of of underpaid pissed off people who are generally low paid, in-experienced and disinterested.
Unfortunatly in this case, It's their word against yours. You probably wouldn't have a case in small claims court. You can't prove anything.
You could try BMW customer services. They're usually helpful and can really put pressure on the dealer to keep you happy.
But on the plus side, it's a really easy touch up job. I've seen new bikes scratched worse than this touched up by a sharpie marker before being delivered to the new owner.
Perhaps you could make a deal with the dealer that you won't persue it further if they have it touched up by a professional. (Not their in-house knuckle dragger with a tin of hammerite)
P.S. Don't worry about the sealant. They all do that. It's just the excess. Pull it off and carry on.