Pagani dont have a F1 subsidiary team like Scuderia Ferrari, from which they can gain progressive engineering resources.
this is precisely why they have to make a race care to beat a lab car such as 599xx.
Pagani dont have a multi billion dollar research and development scheme like Ferrari.
as above.
Pagani dont have a Schummacher to aid them in the development of a supercar.
not clear how effective is schumacher in developing road cars. most likely his role is bounded to the commercial department.
Pagani dont have a Fiorano test track in their back yard to continuoulsy test and tweak their cars like Ferrari do.
Pagani is a far younger company with the smallest workforce amongst its rivals.
Pagani has access to plenty of other tracks, certainly this is not a shortcoming.
Pagani have not outclassed Ferrari by any means. the records they broke (this is the only one) follow simply by the extremness of the zonda r and the zonda program altogether which makes these car not much practical in real world (there is a nice vid by top gear on read using of a zonda, ford gt and ferrari f430...). on the other hand, zonda r has sacrificed roadability as much as a 911gt2rs, except that doesn't have a driving plate, hence hats off to pagani which is nicely implementing what he has learned in his past job experiences in italy.