Actually, anytime you re-provision the container it will revert back to it’s default state and wipe out any updates you might have made. I find this when I update wp-cli to v1.0.0. Restarting/reprovisioning a site sets it back to v0.24.0 which is the included version.
It would be nice to be able to update these components and have the changes saved. Optionally adding components, like Composer, would be great too.