I have not tested this, but I believe you should be able to perform Manual Key Exchange on Linux hosts by running a command against the agent as well:
https://help.hcltechsw.com/bigfix/10.0/platform/Platform/Console/ManualKeyExchange.html
This would look something like:
/opt/BESClient/bin/BESClient -register <password> [http://<relay>:52311]