So, there are a couple of things to note here.
One, the remote pilot certificate is not tied to the registration, and two, you can fly a commercially registered drone for recreation whenever you choose.
Our recommendation would be to go ahead and register for commercial use and eliminate the need to re-register once you receive your certificate and actually start flying commercially.
If you have more than one drone for commercial use, each drone will need to be registered separately and have their own unique registration number. Hobbyist registration allows you to apply the same registration number to multiple drones.
More information over here: https://faadronezone.faa.gov