Not all ComStar/WoB forces used C3i systems. Plenty went without.
The C3 variants are exports for mercenaries and used by the Word of Blake Protectorate Militia which is organized along standard Spheroid lines rather than the ComStar/WoB base-6.
As for why the 'Mech never got a C3i variant, i figure that this boils down to it being "filler". In-universe, it may not have made sense to integrate relatively expensive C3i system into it (going by C-bills, so sorry, 750k vs 250k of C3 slave). IRL, it may be TPTB deemed the design too lowly for C3i or just forgot it.