commerce_checkout_completion message is the only one I see. The order and settings of the individual panes doesn't seem to be there. I wonder if it's because I have some 3rd party modules messing things up?

From what I can tell that's for migrating products and product settings, not really for checkout/payment. And I'm not migrating from one site to a new one, it's for a dev/stage/production workflow so we can export configuration to code and revert it when need be.