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I don't have the MCN to hand, and I've slept since so bear with me if this isn't 100%. I also appreciate that you probably don't have access to this paper and article in the USA.
But Spalding was saying that the difference was in the gearbox, in that the Factory bikes have something to compete with HRC's seamless 'box, while of course the T3's don't. There was also a chassis difference.
The interesting bit was his outline of how Yam's budgets dictate that it would add a mint to produce the same bits for T3 - so as they develop the factory bikes, their redundant parts with mileage left in them get maximised through T3, and filter down. Hence any engine update would be (relatively) fast, while a gearbox lasts a lot longer, so the 'boxes and spares left from '12 will keep T3 going a lot longer.
That's the article in summary as I recall it.