From my limited knowledge the Sport Chrono 2000 was made in two lines. One the regular GP (Blue, white and black dialed versions) and another one co-branded with Ferrari (with black dial, carbon fiber dial, and some others which I cannot recall at this point but all associated to Ferrari's racing achievements).
I may have even seen that particular model you are talking about online, and it is my impression that that particular watch and box set was made up afterwards.
Now, this may be deemed as a bad thing, but if you love the watch (which I do, and I know that they seldomly come by) well I really do not see a big issue as the watch, specially one like this is meant to be worn and enjoyed.
The only thing I would suggest is to ask for more assurances as far as provenance and origin of the watch is concerned.
Good luck and please post some pictures if you decide on getting it.
Cordially,
Alex