I think that Googles entire goal with this is to break manufacturers monopoly on handsets and get android under more central control as no one will be running samsung-android or htc-android on these things
Eh, I wouldn't underestimate manufacturers' ability to attempt to control them. As long as the bus allows it, all Samsung has to do is sell Samsung-branded modules that only work (or only fully work) with other Samsung-branded modules.
Think about the heyday of the PC market - sure, you had vendors selling complete systems, but you could also buy individual components to upgrade, and even build complete systems from scratch yourself. If this tech allows the mobile phone market to follow the pattern of the explosion of the "IBM-compatible" PC market, it could lead to real customer choice and innovation, as long as the general public avoids too much vendor lock-in.
Further, the Android app market already has to deal with the large variation in devices, software versions, screen sizes, etc.; so I don't think this would change it that much. PC software has pretty much always had to list minimum hardware requirements, so I don't see this as being much different, with apps requiring minimums for Android version, memory, processor power, etc.