WOW, a cracked frame on (let's just say) a bike that is a year old and you send your customer home with a new bike? Not a frame swap? That's pretty incredible to say the least!
We do frame swaps. We'll pull the components off a new bike and put the components from the customers bike on the new frame. We then bag up the components from the new frame and label them. Set them aside awaiting the replacement frame. Not much trouble for us. 99 out of 100 we don't have a frame, it's a built bike, so we just do a couple tear downs.
As for this case... well the dealer probably can do it via email/phone, but they probably want to see it for themselves/a trust matter. I'm pretty sure I'd ask that it be brought in as well if it was being replaced. 3 hours though? That's too much. You will indeed need to make at least two trips probably which is just no good. I would talk to the owner of the bike shop if you haven't already. I wouldn't drive for 3 hours on the word of a wrench or POS clerk. It would be terrible if you showed up and the owner told you he wished he could have saved you all the trouble. I think due to distance you would be a special case.
It may be an Orbea thing as well. When we have a problem with a Pinarello the Gita rep is there before we can blink usually. They check things out for themselves and we work together with Pinarello to cut the customer a deal on a new bike. So they might need to have a rep see the frame/verify it or maybe it's protocol for the shop to take the frame? Again, I'd talk to the owner about it. Anything to save that drive.
Nice that it's under warranty, that's a relief. Hopefully they have something in the color and size you'd like.