2-perf,,
I was sure I replied again with a detailed answer to your question but I must've forgotten to submit it.
When the source is MKV or indexed by a flavour of DGIndex, the audio is extracted, added to the audio section, and MeGUI creates a script for encoding "behind the scenes". For other file types it can't extract the audio, so instead it creates a physical script it adds to the audio section. Therefore, rather than use MeGUI's audio encoder configuration for specifying a speed change, you can leave it doing nothing but encoding, and create the script for it to encode yourself.
To make creating the script less of a chore, you can add the
AudioSpeed function and tell it what you need, including the output bitdepth.
From there you can encode as 16 bit flac, but foobar2000 converts to wave "out of the box", and thanks to the
AVS Input DSP, it can open Avisynth scripts and play or convert the audio. If you forget to tell AudioSpeed you want a 16 bit wave file it's not the end of the world. fb2k's converter configuration lets you specify the output bitdepth when it's a lossless type.
Because fb2k can use any command line encoder for converting, you could bypass Avisynth, extract the audio and open it with fb2k and simply convert using an encoder preset you created earlier. I've saved configurations for applying speedup and slowdown with SoundTouch, SoX and FFmpeg. If you want to try foobar2000, let me know and I'll post the command lines for you.