The problem is that a lot of the vehicles (cars and motorcycles) are stuck at port on the west coast. There's a huge back log (about 2 months) due to the union strike.
So the dealers know where the vehicles are if they were already shipped from Yamaha, but they have no idea when they will leave from port. Unless they request from the manufacturer directly to expedite a delivery, which probably has an additional fee. The manufacturer is shipping to the dealer, so the request has to come from them. For an R3, considering it's within the "budget" price range, there is no real incentive for the manufacturer, Yamaha, to expedite these.
But if it's an R1 or R1M, or any other high priced ticket item, then maybe the manufacturer may make exceptions.