The Steam version auto-updates, which can break mods. The Fitgirl repack is a static version (usually v1.04, the final patch). Modders love this because:
Fighting game locals often use offline PCs. Instead of logging into 8 different Steam accounts for a tournament setup, tournament organizers use the Fitgirl repack. It allows instant character unlock, no profile switching, and perfect offline tournament mode (P2 vs P2). Ultra Street Fighter IV-RELOADED Fitgirl Repack