CoreMotion updates in background state

RunKeeper actually does use the audio trick to stay awake. If you open up the app package and check their Info.plist you will see that it registers for the background audio mode. This is how they pull off periodic audio notifications of your distance, speed, and pace. It is also how they stay awake during your run while minimizing battery drain.

If you noticed that the Location Services icon (the triangle in the status bar) disappears completely while using RunKeeper then they definitely are not using any type of location tracking to accomplish background execution. Even activating geo-fences and significant location change monitoring would cause the Location Services icon to appear.

They also aren't using the M7 to stay awake because it doesn't work that way. An update from the M7-related CoreMotion APIs will not wake up your app from sleep. When they app does wake up they would be able to query the Motion Activity and Step history and maybe try to compute something, but I doubt it would be all that accurate.

Finally you should note that the Auto-pause APIs were introduced in iOS 6 before the release of the iPhone 5s and M7 chip. They are orthogonal concepts.