I'm basing it off of the final price (actually production costs * 1.x, x = margin). 40% on a small number is easier to swallow than 40% on a much more expensive item to produce. If the MP's were substantially less expensive, it would help push sales. Now whether or not that generates the largest pile of cash (profit), depends on the specifics (quantity sold * profit per unit). And we know Apple is greedy...I agree with all your points nanofrog. However, on Point #1 about the increasing prices in Intel CPUs in adding cores, coupled with Apple's outrageous margins..... Apple are already making huge margins on all of their products. Some more than others, like the iPad which brings them an almost 50% margin. And that margin doesn't change when economies of scale kick in on the assembly line and manufacturing costs decline.
My point is, with so many new products bringing in large margins, surely they could accept a more reasonable margin on the Mac Pro and not leave the Mac Pro community out in the wind to twist.
In the case of the portable device market, the sales numbers are massive, and even though the price is lower, is still generating a much larger portion of Apple's total profits per unit time than the MP + XServe.
I agree they could do what you describe with the MP's, but as they don't publish the exact sales numbers of the MP and XServe, it's hard to say what's truly viable, as they won't take a loss (or even be willing to accept break even IMO). Shareholders are just too conditioned for high margins given the recent quarterlys. Ultimately, they seem to have shoved the MP to the absolute bottom of the developement pile (well, maybe just above the TV). Human resources are limited, so they start with the most profitable segments first, and move down. New products and delays are increasing the cycle times of the MP and XServe lines. As they've not hired additional people (they certainly have the cash), this lends me to think they're contemplating it's continued developement all together (assuming they don't have their heads up... in terms of being able to see/predict what's happening in the industry in terms of workstations and determine if they're going to remain a part of it or not).