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but that a from-scratch design could be more expensive.
Definitely not. After you reach a certain level of complexity, stripping back a board to build it back up again is more time consuming than laying everything down from libraries.
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apropos, that SBC you linked to features SATA ; ) admittedly, most other SBCs don't.
The first milestone for building a board is always to create design libraries and modify existing ones to the specifications. Once you have those you can build any board out of those components once you match pins up between them. Then you do the signal routing and make sure there are no timing problems. All in all an entire design may be done in less than 12 weeks with the right experience, and the cost is entirely based on time..
Since Genesi have the ability to go from scratch to prototype to low-volume production (1000s per month) and provide firmware and BSP, which is sort of rare in the industry to do the whole thing, costs are brought down this way, too.