“Ponding” on your roof is never a good thing. The additional weight and the tendency of water to find its way through waterproofing requires all roofs to completely drain.
Proper drainage ensures the growing medium will be maintained in an aerated condition suited t healthy plant growth. Basal drainage must also be designed with large rainfall events in mind. The goal is for all rainfall to percolate to the base of the green roof system. Any water NOT absorbed should move ‘underground’ through a drainage layer toward roof drains or scuppers, and then into your rainwater harvesting system (if installed). City codes typically require a redundancy in your drains or scuppers, just in case something clogs them up.