It is a typical strategy of Apple to slightly underspec desirable aspects of a product like hard drive capacity or RAM (...or ports - sigh). That way, they can release an updated version where those specs are bumped, resulting in a product that is perceived as significantly better instead of just slightly better in comparison to the previous model.

I think it's also about using components that give you the largest gross margin - A slightly outdated model of a component will always be cheaper and more readily available than the cutting edge model - which further carries the risk of being less broadly tested.

An in-between step is often to offer that option (like a larger SSD), but at significant additional cost. Particularly with things like RAM, apple sometimes charges you more than twice the regular market price: Getting a Mac Pro, for instance, you pay ~1k € extra when jumping from 6GB RAM to 32GB. Buying 32GB of RAM (yes, ECC and everything), sets you back 400€.

Their SSD prices have gotten slightly more reasonable lately (buying the regular HDD option, selling that drive and buying your own SSD often saved you hundreds), although they're still a good bit off - especially considering that Apple buys OEM from Toshiba and in bulk.

My personal conclusion is always to buy the bare minimum configuration and upgrade myself - I purchased a Macbook Pro 17" at the smallest configuration and added an SSD and an extra regular 1TB drive. Will probably add some RAM later this year. Had I gotten all that at Apple right away, I would probably have to pay 50% extra (although they don't even offer the option of exchanging the DVD Drive with an HDD).