I would agree with your first point - without a doubt Alonso has benefited.
The Ferrari wasnt as bad as press wanted us to believe, and while FA flattered it slightly - Massa made it look far worse than it ever was too.
I would still say the Ferrari was the best car given all conditions / circumstances & tracks.
(and the new scoring system definitely benefits those who score most frequently even if they rarely win the very big points)
If it was the best car then they would not be needing others to having problems The Ferrari was a dog to drive until Spain, anyone could see that from watching the incar. Since then they have got on top of it and have got to a decent level but never in a position to say they have the best car. Take away the rainy races which negate a poor car somewhat then you can't really be saying Ferrari have had the best car surely?
As I said if it was not for McLaren and Lewis having problems then he would be well ahead IMO.