JobScheduler is creating and starting for a scheduled job or jobchain-node a separate process. The number of parallel processes can be limited. The workload of the job has no impact on JobScheduler. Sometimes the size of the logging-file could have create a problem due to some restrictions on the used database.
If the program which has to be scheduled by JS can be started in a shell (windows or unix) the job-type must be a shell-job. All programs, which are started by cron or taskplaner should be running in the shell-job of JobScheduler as well.
It is important to keep in mind, that JobScheduler is running as a service (windows) or as a demon (unix). JobScheduler must have at least all the requiered permissions for accessing the resources, which are needed to execute the program.
If it should be not possible to start an executable in a shell it could be possible to implement a wrapper (e.g. in Java, ...) and execute this program as an api-job (like the "standard" jobs).