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To be specific, I would like to be able to set LimitMEMLOCK through the rancher-system-agent as it setups the service files for other elements

that’s not an environment variable, that’s a systemd unit configuration option. There is not currently any way to alter the systemd until files; you would need to provide your own drop-in file on the node to add or override any fields in the service unit that you want to set.

everytime i’ve altered the env files listed in the rke2-agent.service files or the service file itself, the changes are removed after anything triggers a reboot or system agent change - how do you prevent this?

Don't alter any of the files created by rancher, it will put them back periodically. Create another file to add or override what you want to change.

is there a list of files that the rancher agent manages wrt systemd and env files? This would be a great addition to documentation without having to trawl through scripts or just trial and error

if its a RKE2 config file and exists, but you didn’t create it, assume it’s managed by rancher