What's the deal with the variants / modules thing? Why are the exteriors the same? Will there be new packages?

The EMP and cargo versions of the Avenger are currently being offered as single unit ships because the system that allows captains to switch modules is not yet active in Alpha 2.0. Once that system goes live, separate cargo, bounty hunting and EMP modules, like those offered in concept for the Retaliator, will be made available. For now, pick the Avenger you most want to fly so that you'll get to enjoy it in the 'Verse!