Yes, you can create Marketo only custom objects. This is done in admin->database management->Marketo custom object. If you do not see this entry in the admin, call support and it might be related to your licence.
BUT, you will not be able to capture form data in custom objects. adding data to custom objects can only be done through API or imports. Neither can you upsert CO data in a flow step, in a "fills out form" triggered campaign.
What you want to do can be achieved with some custom devs. Some of the webhook platforms available in the launchpoint might also be able to do this.