I don't own a Kubota, but from one of the angles, it looks like the hood is slightly rounded. If that is the case, could the cross bar have made the dents on the sides of the hood without denting the top of the hood? The top looks unharmed.
As far as the dealer doing it--nothing would surprise me, however that's a part of the tractor that you look at all the time when doing loader work. Those dents are not impossible to overlook, but it seems unlikely to me.
Keep us posted Viper--it's an interesting issue and I agree with not replacing/fixing until you are sure of the cause.
Good Luck
Bob