You mean by clicking the "execute" button on the Manage > Jobs page? If that's what you mean, the answer is simple:
Since this uses the managementService.executeJob method (Forced synchronous execution of a job, see javadocs), the job-executor is not involved in this, the job will be executed synchronously, using the thread that calls the API (in this case, a tomcat-container thread). So even if the jobExecutor is not enabled on explorer's engine, you'll still be able to execute jobs manually.