If I want to run the fleetdm binary, can I pass in the env var during command runtime? like:

./fleet_linux_amd64 PASS_ENV_VARIABLES_HERE

how would it look like?

Please see the docs. Many of your questions are answered there. https://github.com/fleetdm/fleet/blob/master/docs/2-Deployment/2-Configuration.md#using-only-environment-variables