I think the note is clear in saying that the jobs that are submitted directly to command-line works that way. However if it uses applications like VA it uses the submitting user.
Note: Jobs that are sent to the command-line job runner run as the user of the distributed
in-process scheduling server process, rather than as the user that scheduled the flow.
Jobs that are sent to applications are run using the application’s submission methods.
Jobs sent from SAS Visual Analytics Designer run as the submitting user.
If you want to schedule jobs there are other alternatives available as well, may be you can try that.
You can still check if there is an option to change the submitting user by emailing the details to SAS technical support team at email@example.com