The good news for some of this is that the environment variables for automating the commissioning steps function in the base platform as well as the Docker images. The environment variables you need are ACCEPT_IGNITION_EULA, GATEWAY_ADMIN_PASSWORD, and possibly IGNITION_EDITION. More details here, although like I mentioned, you can supply these particular environment variables to a regular installation of Ignition too..
EDIT: I should also mention for clarity that if you do the above combined with restoring your GWBK (with the skip-gateway-contact option, documented here), it should skip commissioning and restore your gateway backup, all in one shot.