If you plan to install large mods (like the Mortal Kombat 9.5 overhaul), some modders recommend the FLT release. Because FitGirl uses compressed .arch00 files during install which are then expanded, very rarely a mod installer expects a specific file structure that FitGirl modifies. This is rare for MKKE, but happens in other games (e.g., Dark Souls ).
The fundamental difference lies in their purpose within the digital scene: