I am not Apple, but I did study economics for a long time, and my answer would be: price discrimination.
In an ideal world, sellers would be able to set the price of their goods individually for every consumer. Everyone has a slightly different willingness to pay, and if they could somehow charge everyone their exact price, they'd make the most profit.
But that's obviously not possible, so they set prices. In doing so, they lose some potential revenue: people with a higher willingness to pay get a deal, and people with a lower willingness to pay don't buy at all. So there's money left on the table.
By selling two (three, if we count both standard trims of the Pro) versions of what is essentially the same product, but at different prices, Apple can't extract some of that money left on the table. People with a low willingness to pay buy the MB. People with a slightly higher willingness to pay, who would otherwise leave money on the table, buy one of the "Pro" models.
This is just an educated guess, but I'd say Apple figures the benefits of extracting that extra money from consumers trumps the costs of keeping two production lines going.
Feature differentiation as a mechanism for creating price discrimination isn't straightforward. For example, the more willing to pay consumer will weight the additional cost vs the additional benefit of the higher trim. A rational consumer wants to grab as much of the surplus as he can, just like the seller. At this point, it's more about consumer psychology than it is about rational actors.