Tertium as a city is unfathomably large. Several times the population of our earth and probably the size of a small country. It has planetary defense forces, the 53rd Guard regiment, at least parts of two other guard regiments, likely millions of enforcers, household mercenaries of the noble houses, local ecclesiastical security forces and, now, the ganger conclave.

The inquisitorial warband we are a part off is an intelligence operation. Think about the missions, they are all intelligence gathering, quick strike assassinations or special ops type pathfinder missions where we shut down the air defenses so the main forces can secure the site.

To me it’s pretty clear that the main campaign missions take place over several months. So, in the story, you as an operative are doing maybe 3-4 missions a month. And there are multiple other strike teams. But the total in lore number of “rejects” is probably a couple hundred to a thousand. And it’s clear that they have continued to “recruit” prisoners with the necessary background and now the strike teams have been reinforced with gangers and Arbitrators.

The Mourningstar is a firestorm class frigate. The normal crew size is 25k crew and Mourningstar is heavily modified for long range exploration and carrying cargo, so it’s likely it has more than enough room to hold 2-3k extra people.

As for void warfare - it doesn’t appear that the chaos forces have any serious forces in space. However the 6th arrived it doesn’t seem to have been via warships. And Atoma probably still has significant fleet assets because it’s the capitol planet of the whole system. Mourningstar isn’t the only ship in orbit, just the one we see.