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I just tested it here, and I see no difference in CPU usage on my end between this setting on or off. The amount of calculations is also identical; the only thing that might influence things is that when spreading the load over multiple cores, there could be more cache misses. Plus there's some synchronization code, but that's really negligable.
How do you check the CPU usage in Windows? If that's with Task Manager, please be aware that the number that Task Manager shows can be quite far off from the real CPU usage.
But: I see that you wrote this: "The number of parallel threads is set to 6.". With the "separate thread" setting checked, that would mean that Stereo Tool is in fact using 12 threads. And since there aren't that many CPU cores available, chances are that the CPU is using Hyperthreading, which might increase the CPU usage. So I recommend lowering the number of threads. The newer version of Stereo Tool works with CPU presets, and won't offer you any settings that use more cores than what are availalble.
Initially I tested with Task Manager indeed, but I now tried with both Process Explorer v17.06 and HWiNFO v8.30 as well. Also I have decreased the number of parallel threads down to 4 to match the actual number of available CPU cores.
I can fully confirm that all three measurements are consistent and reveal a significant CPU-load increase (goes up from approx. 35% to 45% total CPU load) when enabling "Use subthread per channel". It's actually noticeable, as the CPU fan increases its speed as well. My computer is an HP Probook 650 G1 with an Intel Core i7-4810MQ and 16 GB DDR3 installed, running Windows 10 22H2. This issue reproduces regardless whether audio is played or not.
I tried disabling FM-processing and the CPU load difference remains proportional when switching the setting on and off.
UPDATE 17-08-2025: This issue also persists with a fresh ST installation (factory defaults). It appears that disabling this setting makes fewer resources available to ST, as the processing load reported by ST increases in inverse proportion to the CPU load reported by Windows.