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I think he i saying there is a different 10.9.1 build number for the new Mac Pro. I have not seen any info on that either way though.

Exactly!

It includes all updates from OS X Mavericks 10.9.1 plus system-specific enhancements and fixes to improve the stability and compatibility of your Mac.

Never seen a late OS X update for one product specific.
 
It is probably because of the dual GPU in Mac Pro. Probably, the system is updated specifically for that machine to take advantage of the GPUs.
 
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