According to our docs here you should be able to create an organization owned project via the CLI by using the following command:
domino init --owner myOrg myProject
Unfortunately, there is a bug that may prevent this from working on some deployments. Instead, you can initialize the project via the CLI using the following command:
And afterwards you can go to the project's setting page in the Domino UI and transfer ownership to the proper organization.
If you encounter this bug and it's a problem, please let the support team know.