FFT3DGPU cannot work in MT mode 2. It should be possible to patch McTemporalDenoise to enclose each call to FFT3DGPU between SetMTMode(5).(...).SetMTMode(2). However I don't know if it really works and if it is efficient.
The best thing you can do is to encoding multiple videos simultaneously to saturate the CPU given a reasonable memory usage. Check the overall FPS, maximizing the CPU load does not necessary means that the frame throughput is optimal.
Another lead is tweaking the MCTD settings to accelerate the whole processing. Or you can remove MCTD and use the QTGMC internal denoiser. BTW I don't really understand what you are trying to achieve with this script and why you are applying RemoveSpots and LSFMod on interlaced material.
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