@2-perf:
Audio conversions are handled in AviSynth scripts as well, so if you are able to edit the generated audio conversion script before starting the job in the queue (i.e. if you find its location), you could manually add ConvertAudioTo16bit() ... the tempo conversion will have converted the audio to float before output. MeGUI might add a selection here to add a sample type conversion in the codec configuration.
Unfortunately, I don't see a CLI parameter combination for "flac -d" that would force flac to reduce the resolution while decoding to WAV, only while decoding to raw audio (--bps=16). But e.g. Audacity would be able.
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