Like Dan said, that's the only thing that really makes any sense, but IIRC there is never a single mention in the game (dialogue, journal entries, etc) that the "human Reaper" was some sort of core or "heart" that would be at the center of the larger cuttlefish looking Reapers... it's just referred to as a "human Reaper" multiple times. If taken literally then one would indeed assume it was supposed to be a giant space-borne entity like the other Reapers but in a form loosely resembling a human. This idea really doesn't make any sense for the reasons outlined above. It was sort of theorycrafted by fans into the "core of a Reaper" idea.
In other words I'm agreeing with you, I'm just pointing out that the concept was kind of bungled by the writers and/or development team because it really wasn't made clear.
Well, given that a Reaper will dwarf any alliance ship short of the DA. It's highly possible for what you saw will fit inside as the core, just that the outer shell have not been fitted.