Visibility of multiple networks can be used to refine the position.
GPS takes time to acquire and isn't always available indoors. SSID method is quicker, and it's most likely the method your phone uses to get the position first.
As you say, it’s a method to get a coarse location and then refined using GPS which by the way does not really take time to acquire once you have downloaded the almanac and have the coarse location.
So this ‘allows applications to track location’ actually allows applications to track coarse location which then does not allow them to refine using GPS.
GPS takes time to acquire and isn't always available indoors. SSID method is quicker, and it's most likely the method your phone uses to get the position first.