Code related to this issue has just been checked in; Renegade wrote in revision 238:
Issue #342: Operator=
Removed Occupants-related section, integrated buildings into the passenger section. If passengers don't work by default, add InfantryAbsorb=yes to your building.
Also made Operator parsing only fire if the building in question is currently online (i.e. has power).
Maybe an temporary armor bonus for the infantries inside the domain?