I'm not sure on the technicalities regarding the actual speed differences but from what I understand the differences should negligible. From my experience, the main difference between the two activities really comes down to configuring them. Auto-OMR will try to identify entire regions at a time whereas the standard OMR will require you to manually drag boxes and configure each zone which can be very time consuming if you're dealing with a lot of check boxes. If you are really curious, you can probably just test it out with your VAR kit and see if there's a meaningful time difference between the two activities. 

Note: If you use the standard OMR and you have multiple areas on your page that you want to capture, make sure you have just one OMR activity with all the zones contained within it and not separate OMR activities. That will maximum your system performance.