It's not "in place of" a pistol. Pistols aren't general issue, and this isn't a game, you don't have 3 slots with various guns to fill each slot.Apparently the USMC Force Recon, SEALS and some Special Operation Groups have the 11.5" barreled M4 Commandos in use with some members in place of the M9 pistol.
Or are you telling me they carry a rifle or an M4 carbine.....AND a Commando?
Do you mean the Mk 18? Not really a Commando, though I think Colt may still make Commandos.
And yes...Spec Ops gets odd stuff depending on mission. Next mission they may carry something else.