You clearly didn't see the shot he played to get out for a duck against them
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You're right that it's crude and arbitrary, although I'd argue that including them is even cruder and comes from the equally arbitrary judgment of the ICC. It's obviously crude to suggest that not scoring against Bangladesh and scoring against Bangladesh are of the same value but I think it's even worse to suggest that scoring against Bangladesh and scoring against England or Australia are the same.
You seem to be asking "why exclude them?" and want a definitive answer, I'm just asking, "which is better out of excluding and including them?" Neither are perfect, obviously, and an average will never be able to demonstrate the details of a match such as those you mention above relating to Bresnan and KP.
But I think a figure without them is better than the alternative. Irfan Pathan's figures including Bangladesh give an absolutely horrendously inaccurate estimation of both his performances at test level and his general ability, whereas his figures without them give a pretty good one. Is there any cricketer for whom the reverse is true?