MMM is using the slot236 to function properly
USBLoaders are using the slot249 to function properly
that's providing different features for different programs.
The Wii has 257 slots where "IOS" (system files) can be installed into. some IOS are specific to certain programs or games, some others are specific to system menu, etc.
not all slots are used, but only one IOS is loaded at the same time. Other installed IOS are not affecting the "current" loaded IOS for that program.
A program requires one IOS which provides the hardware communication functions to interact with the console (wiimote, hdd, memory, wifi, etc.).
MMM uses the IOS installed in the slot236 to get memory access to extract and install WAD's file content into the console.
USBLoaders uses IOS installed in slot249 to get USB access to load games from usb instead of disc.