MKVToolNix solely operators on the container level, not at the codec level. It cannot convert from other codecs (e.g. AC-3) to WAV.
If you have PCM track, you can use mkvextract to extract that one from a Matroska file into a WAV file. For everything else you’ll need other tools such as eac3to or ffmpeg.
The Windows store version does include the CLI tools, but due to how packaging for the store works you cannot use them, unfortunately. See this FAQ entry for details.