If you are using a decent smtp plugin that sends out your emails as from your website instead of the default from 'WordPress' - then it is probably a good idea to deactivate the SP email overrides. However - you probably only actually need to turn off the use of the SP New User registration email which has been a problem for a small handful of people as it may attempt to access a data item that no longer exists. This is following the recoding by the WordPress team of their password handling.