You talk about integration, and whole systems, but want to break it down to individual parts? Sorry, maybe the definition of "integration" goes beyond just "this phone fits with that dock" level of integration. Maybe cross-platform sales and market presence in multiple channels leads to better sales for the company as a whole.
We're talking about the valuation of the ENTIRE COMPANY, not just one division or group. So look at it that way...
What reason - other than hope for future growth - can you give for Apple being more highly valued than Microsoft? Why is Apple's future brighter than Google's future?
The biggest one: Microsoft's consumer profits are almost exclusively tied to the desktop, while the future is in mobile computing. It's already happening, with notebook sales eclipsing desktops, and now people are realizing phones and tablets can do the job too.
Apple has been concentrating on mobile computing for years, so much that they even delayed OS X Leopard to concentrate on iOS for the iPhone. Apple has a vision on how to make money in the mobile world, and it's working.