Automatic configuration is indeed the preferred mode of configuration.
It eliminate human errors that could potentially affect mail flow, allows our support to handle day-to-day issues faster and allows the customer to immediately enjoy every new feature and fix.
Manual mode is there to support niche cases, where customers do not allow any application to make changes to their Exchange Online and are mandated to conduct these changes manually. This is very rarely the case and less than 1% of Check Point's customers use Manual Onboarding.
In case you are not sure if you need Manual Onboarding, please don't hesitate and contact support - they will gladly help.