I know that BCContainerHelper already contains a method to Publish-PerTenantExtensionApps (https://github.com/microsoft/navcontainerhelper/blob/ed6976186a082d492a95e8f59271b3bc13044d8e/BcSaaS/Publish-PerTenantExtensionApps.ps1) that uses the Automation API (https://docs.microsoft.com/en-us/dynamics365/business-central/dev-itpro/administration/itpro-introduction-to-automation-apis)

It is required to add in the Automation API functionality to upload an Extension that contains breaking changes in the schema setting SchemaUpdateMode = ForceSync. Obviously, this will work only in a Sandbox environment.