I'd say Lowndes and Whincup are a big part of their success... Also, they invest heavily in talent, like snatching Burgess from Jim Bean Racing...
From what I've understood, they have the same basis, but apart from the few standardized parts (mostly along the aero and drivetrain) they can build up the car within the regulations how they like... The rollcage alone can help massively with rigidity, then there's the engine, the front suspension, airdam design and so on - even ducting can make a difference if Larkham is to be believed...