First, find out if the Spyder has been officially put in use. The dealership should be able to tell you. If it has been put in use you need to know the date because it will affect the length of the 2 yr factory warranty as well as the drop dead date by which you must purchase a B.E.S.T. extended warranty if you are inclined to do so. You have until the 2 yr factory warranty expires to buy the B.E.S.T. extended warranty and the prices vary so don't buy without shopping around and you don't have to buy it from the dealer who sells you the bike.
Second, do not waste any money on an alignment unless it is done by a qualified technician who knows what he is doing with the Rolo Laser Alignment System. According to this link, the only KY dealership with the Rolo system is in Lexington:
http://www.spydercomfort.com/dealerky.htm.
Third, I apologize, I don't know what you mean about reflashing unless you're talking about the Engine Control Unit, ECU, in which case I don't believe dealerships have any capability to do so but am not certain. Do you perhaps mean updating the BRP Connect software? The dealership should be able to do that and you should be certain the lastes update has been done. There should be no charge for that.
Fourth, you say the battery was dead when you initially saw the bike. Look at the decal on the left side of the swing arm and it will tell you the month and year the bike was manufactured. If the bike is more than a year old try to get the dealership to replace the dead battery with a newer one. They obviously didn't pay much attention to keeping the battery charged while it was sitting around. Try too to get them to throw in a Deltran Battery Tender Jr. and connect the fused pig tail to the battery.
Fifth, make sure the hard copy of the operator's guide is included with the bike. It should be in a plastic pouch stuck on the battery cover door behind the liner in the front trunk. Read the the thing thoroughly at least twice.
Sixth, be certain you get two chipped keys including a small plastic tag that has the key numbers stamped on it.
Seventh, ask the dealership when the first service is due and if they tell you anything less than 3,000 miles make them show you in the operator's guide where the first service mileage is shown.