Not just the ~20% retail margin, but also that Intel as a company has a 60% gross margin for themselves. Then consider there are huge overhead costs that don't exist for Sony: the design of the CPU and GPU was done and paid off by AMD on their desktop products, and the wafer startup costs can be diluted over far more wafers than a single gaming GPU die would do, because PS4 will sell much more. Finally, a gaming GPU includes a board (not used), shroud (not used), ports (considered elsewhere) and also includes memory we're considering seperately, as well as a retail box, manuals, support and warranty coverage.

the ram i even cheaper as i thought even if it's easily the most expensive stuff in the console. i would have used that too, then

and damn blu-ray was so expensive in the past it's crazy.

not bad. $450 at launch, while praying for $300-$400?

The OP article was already overestimating HDD cost, entry level ones can be found at little more than $40 RETAIL price. The MoBo can be cheaper than cheap general purpose ones we commonly buy, as it has to be fitted with a single set of standard components without expansion slots (except maybe one more RAM slot for possible last minute RAM size increase and/or to expand it for devkits), PSEye can be currently sold at RETAIL for ~50 Euros in Europe without bundled game, and an updated PSEye won't be too expensive in a few months, as the tech necessary is already existent and cheap. About RAM price, it should drop quite quickly as usual from current price.
About CPU price, you made the wrong comparison: current AMD 8 cores are high end FX versions, using heavyweight cores, while both XB720 and PS4's APUs will use lightweight "Jaguar" cores. To make an example, IBM and other POWER partners already make POWER 7 multicores with 16 or even 32 lightweight cores cheap and fresh enough to be used in routers and gateways. The GPU will be mid-range, not high-end (as all the streamlining and HW standardisation done in consoles allow mid-range chips to give higher performances than on general purpose, but bloated PCs with wide variety of configuations that allow far lesser optimization). Also the production cost estimate for DualShock4 is quite high.
But in the end yes, including all the things missing in GAF / Beyond3D estimate the costs could exceed $400 minimum, but not so much and closer to $400 than to $500.
Last but not least, the later PS4 will launch, the cheaper its costs for the same HW.

Well put.

Though, I think you are lowballing the new PS Eye's tech a tad. You are probably right about the CPU, though I still think their estimate might be just a tiny hair low then.

The new Dualshock is adding a lot more tech, so I am going assume I am safe with that one, if not a tad low.

I think the mobo cost would be higher than a standard PC mobo because the design is custom fitted to the equipment and thus has more R&D costs involved as well as custom manufacturing required compared to the standard PC mobo sizes and things.

All-in-all, this is a much better launch cost for Sony than PS3, so that is very good. But I still feel like the production costs will be closer to $500 initially, while going down a lot over the first two years.

Only time will tell, since we have no idea what the exact components of each type are being used. Higher quality/higher performance/more custom parts would obviously raise costs.

About MoBo costs, there are two aspects: you correctly say that a custom and highly optimized MoBo has its higher costs, and this is true, optimization costs, a console architecture must last longer than an off-the-shelf MoBo, this thing alone costs, not to mention other important things like heat dissipation in small cases, that adds design costs too. Design, though, is a fixed cost and it's spread on all the units produced, while a custom MoBo, fit with just the slots, sockets and components strictly needed will still have lower components costs, the two things quite balance each other, with lower components costs prevailing in the long term (and this is part of the cost drop as time goes by you correctly mentioned). But yes, higher design and optimization costs will affect more the first batches produced, so it's not unlikely that you be right about initial costs. And hey, about this issue, it could also depend on how Sony decides to account for these fixed costs! They could decide to spread them in a greater or smaller measure on the first batches, depending on which fiscal years and quarters they prefer to look better. About the DualShock, it all depends on how mainstream and cheap the tech present in it is, and how cheap they'll be at the end of 2013 or the beginning of 2014.

There is no way the APU+GPU will cost more than $100 per chip for Sony.... the Jaguar chips is cheaper like a hell and the GPU is not a top high-end... it's middle.