There’s not, to my knowledge, any guaranteed delineation between “stuff that gets configured on rebuild” and “stuff that gets configured on container start”. That is, for example at the moment UNICORN_WORKERS only gets passed into the container via the environment on boot, however in the future we may need to mangle the container image at build time to apply the setting for some reason.
Taking a quick rummage around, it looks like LETSENCRYPT_ACCOUNT_EMAIL does, indeed, get used in the image build process, so a destroy/start cycle after changing that setting in app.yml wouldn’t be effective.