Everyone here should still be within their 30-day return policy, and so getting an adjustment shouldn't be a problem. After all, you could always return your SP3 and repurchase, and if they don't let you do so with your existing machine then that would just cause them a return. I've found the Microsoft Store staff to be very accommodating, and I'm sure they'd rather do an adjustment than take a return.
Also, there was a similar bundle on launch day of the Type Cover, case, and Microsoft Complete for $249 (which I purchased) and I believe one with Office 365 as well. So I don't think this is anything special.
Regarding stacking educational discounts on top of these bundles, they're not really supposed to since it's already discounted. I convinced the manager at the Microsoft Store I purchased at to adjust the price to reflect my wife's student discount, but he had to really work to get the additional discount applied. I ended up getting a very good price on mine. Again, I found the staff to be very helpful.