[Hodar]

How much of Apple's motherboard R&D is done by actual Apple employees in Cupertino and how much is done in Taiwan by partners kept on a very short leash?

Very little design, if any, is done outside the USA. Notice the SSD on the laptops are exclusively Apple - they are not commodity SSD drives. The iPad, for example, has 4 motherboards, one in each corner for symmetrical weight distribution. The iPad is perfectly balanced, up/down as well as each corner. This wasn't an accident.

[dennisw]

Apple motherboards are Intel (reference) motherboards that are rejiggered to Apple specifications. Plus a few interesting chips may be added. Intel has FoxConn do the actual manufacturing of Intel mobos and Apple likely would do the same for its Intel mobos.
http://www.atomicmpc.com.au/News/148502,intelfoxconn-alliance-could-cripple-asus.aspx