Wait - you say custom flash costs more than bulk flash, yet you say that they save from custom flash?
SSD is a big cost contributor (at least for Apple) - you can tell by upgrading their other computers' SSDs. Plus, there is the R&D cost, as well as the cost of using an entirely new chassy (the old ones are pretty much made bulk by now).
RAM may be soldered, but there is more standard - I'd say the costs would be equal, if not heavier on MBPR's side.
Lack of optical drive is kind of made-up for in that Apple basically needed to design the "internal chassy" from the ground-up - rather than just sticking random parts in random places.
And my issue with the OP's argument was that he brought up a point without providing proof - then argues that we need to provide proof against it. This is classic probatio diabolica, and an often-used technique of Internet trolls.