init
A wrong key writes nothing and exits 3.
--region us --api-url https://api.eu.getlago.com is a usage error, exit 2, not a silent override.
whoami and doctor
whoami prints the organization (name, id, default currency, timezone), the profile, the mode, and RESOLVED_API_URL, the host requests actually go to. --output json adds api_url (what the profile holds) and region. doctor reports the same value as one of its checks, next to permissions and authentication, and --bundle writes a sanitized archive to attach to a support ticket.
version and upgrade
SPEC_VERSION is the Lago OpenAPI version the binary was generated from. The binary does not self-update: upgrade prints the brew upgrade or go install command for the latest release, matching how the binary was installed.