Components like the CPU and OS might be designed in America, but it's the higher level software development and hardware design that takes these largely off the shelf parts and assembles them into an actual product, and in the case of Nintendo that happens in Kyoto, not Silicon Valley. Is that really any different from say, assembling a piece of furniture out of materials and components sourced from around the world? Without the product design and assembly all you'll have is a collection of wood and nails lying about.
Same with the N64 - it might have been an SGI designed system at it's core, but through the guidance of Nintendo which developed the higher level industrial design of the console, the controller, the concept of using carts over discs, some of the more lower level OS functions, and of course the user facing software like Mario 64, etc. All the things that actually make the N64 the N64. SGI didn't decide to make a games console all on their own.