If your EPO policy is set to have that option enforced (which it sounds like it is), then it will be re-enabled at each policy enforcement time. You would have to manually take these same steps each time.
It sounds like you need to look into setting up some proper exclusions to let the process run without interference.
The set CPU % works by taking a sample of CPU usage over.. 10s I think? maybe 15s, and it determines the % from that. But once this is done, it does not dynamically change that % to reflect 20% overall CPU usage.