The “Nyquist Prompt” is a general effect that allows you to run “Nyquist” commands.
“Nyquist” is a computer language designed for audio use.
There’s no big difference between running Nyquist code in the Nyquist Prompt and running it as a plug-in. Plug-ins have the added convenience that you can install them and they are then available any time you want them.
M4A is a lossy compressed format. Lossy formats are not not good for this because they lose much of the high frequencies. To retain very high frequencies you really need to be using a lossless format such as WAV or FLAC.