None of the consumer devices I've developed have patented logic boards. Not Kindle, not SHIELD, not Cisco CUE. Maybe Apple does what you suggest, but I am extremely skeptical.
Apple produces their own ASICs and CPUs already. And the dream has always been to pack a high level of integration at the lowest possible cost. Some SoCs have PMU integrated (power management unit, in charge of regulators and sometimes battery charger), but most have a separate PMU because the time to market suffers when you do mixed signal designs.
As for fab yields, it's all manageable. I currently work on a very large ASICs. 350 mm^2