The polling rate doesn't change in Set Point. It's dependent on the profile that's detected. How would you check, otherwise?
The reality is that if you use multiple profiles and opt for 'automatic application detection', the Control Panel 'mouse properties' will always have 'enhance pointer precision' ticked if your 'general' setting in Set Point employs the 'use OS native drivers etc.' option. If you disable 'automatic switching', and check 'mouse properties' from a setting that has the 'use OS etc.' unticked, you'll see that Windows doesn't overide the Set Point settings. The question remains, how would you check for polling rate in 'mouse properties'?
The other thing I've found is that Set Point has to be open for the auto detection.