Youre right, the Program works. But this Program didn't make Magic Desk Cartridge *.bin
With the cartconv.exe from the vice-emulator you can convert the .crt file to bin.
I use this program to genaerate MagicDesk64 .bin and .crt files: https://github.com/Solo761/C64CartBinCreator
Most I freeze the game with action replay, "backup" the freeze to disk, export the freeze with dirmaster from style and then I convert it with the tool to magic desk.