This project is significant as the program used by many GUIs like that. I do find it very easy to mux a new file while replacing the audio tracks using the GUI but it obviously isn't designed for advanced batch processing so it does get tedious if I want to do the same thing to several files. It is a GUI that supports the more advanced mkv features well, but not simple batch processing. The two use cases are difficult to merge well and command line tools are great for batch processing.
For advanced batch processing I go into python.