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If the MBP with the case is smaller then this:

Internal dimensions (HxWxD): 14.5 x 10.5 x 1.5 in./36.8 x 26.7 x 3.8 cm (non-adjustable)


Then yes it will fit inside the bag.
 
I just bought that bag and plan to use it with my incase neoprene on my MBP... in a review on the Apple website someone mentions that the computer fits nicely in the space, but that they still ues their neoprene case, which leads me to believe the MBP will fit in it with a case on it. Nice a snuggly, I'm hoping.
 
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