Bootloader leave Arduino ready to receive the firmware uptate - during 8 seconds. . For transfer the firmware used MjoySetup.exe - tab Firmware (as in F15Sim instructions or there https://sites.google.com/site/mmjoyproject/prosivka).
Done this Arduino became a HID (Human Interface Device), and use Windows native drivers.
And the "joystick"?
Is the "MMJ-Reset" you see in MjoyStup.exe,
Don't has buttons or axis because is your option set how many buttons/axes want, as well what "joystick" name (up to 10 characters, I think), after choose use the button "Save Settings for Device" (and ca reconfigure when want).