If anyone is wondering it's "fixable" if every time you open the script gui to delete the partition letter (c) and then again writing it in lower case. I also changed the location of the mkvmerge.exe to another partition and then it's when I figured that out.
haha, before opening this thread I went in the script itself and wrote a few lines that I thought were missing (just by comparing the other similar code in the script), I added a button to the gui that was not triggering any browse window to select the mkvmerge.exe location like the x264.exe and x264_10bit.exe were doing in the default script - Tho I really believe that there should have been a button for mkvmerge.exe but either the author of the script forgot to add it or decided that adding it will make the gui extended horizontally and would leave an empty space above the button like in the bellow picture of my experiment.
But I did not just add stuff to the default code, I also changed some of the code that I believed was incomplete, to my surprise even tho I changed some of the code it still worked the script was encoding with audio after using the workaround I mentioned in the beginning of the post.
Still I would like if anyone has some programming knowledge to take a look over the default script and write it so that you don't have to do the workaround every time you open the gui. And there is another small problem, using mux audio will convert the video in an mkv instead of mp4 even tho you have selected the encode name to be encoded as an mp4 (I suspect it's because of the mkvmerge.exe code).
Well that's about it for now,