Don't get caught up in the believe that the MUL is the end all be all. TPTB have previously stated that the MUL is merely a tool to help players create units/matches quickly and shouldn't be used to determine in-universe statistics. Not to mention that the MUL is constantly evolving with corrections being made, new units being added, etc BUT there will always be plenty of variants, prototypes, etc that will never be added because they haven't (and likely will never) been fleshed out. For example, several sources mentions that there are numerous variants of Unions but have never been fully (or even partially) fleshed out.
The SLDF likely brought several Model 96 tugs with them from the IS, the survivors of which were inherited by the Clans before they started building their own variants if not outright new designs that incorporated their own design philosophies. For example, if their new tugs were considered non-combatants, they would likely have stripped most, if not all, the armaments from their Clan designs.