No it wont remove the mat zones, just what's connected to them, ie the textures, it cuts down slightly on the file size and loading the cr will be faster as its not looking for map images in your textures folder

Tools:- Win10, Dell XPS8900, ZBrush, Marvelous Designer 11, Hex 2, PSP8. PSP 2019 Ultimate, DAZ Studio, Affinity Photo, Affinity Designer, Filterforge 11, flowscape,  Classic UVMapper, and several headache tablets.