Set up a system agent and configured Arcanist's certificate. When running:
echo "{}" | arc --conduit-uri=https://code.pageuppeople.com call-conduit user.whoami
received:
{"error":"ERR-USER-DISABLED","errorMessage":"ERR-USER-DISABLED: User account is not activated.","response":null}
Replaced the certificate with that of a normal user and the user.whoami call worked correctly.