The second thing is that, at the last minute, the DomZ go into detail about why Jade is so important to them. Jade’s parents stole their lifeforce, which they call “shauni” (which is, not coincidentally, Jade’s chosen codename when working with IRIS), and somehow either implanted it into her as a baby or a foetus, or created her from it. In any case, the DomZ’s harvesting exercises are essentially a life support system while they attempt to track down where their shauni went to. The shauni is apparently very powerful; Jade channels it at the end of the game and single-handedly shuts down the DomZ’s harvesting and returns everybody to Hillys. So your speculation is right – the DomZ believed that their shauni has waltzed right into their base and that they were on the verge of renewal and ultimate power.

Interestingly, the standard battle theme has a choral rendition of the DomZ’s desire for the shauni to be returned to them, which you hear as a chant in the DomZ’s base. It’s very interesting to see the sound design support the plot in this way.