In order to use the Genesis/Final Chapter/whatever finishes first engine, we'd have to modify it heavily to allow for underground levels and an interior view of your colony (a planned feature for OP1; if we do it maybe we'll include people moving around/etc).
(The following refers to Genesis as that is the only OP3 I am familiar with, and seems the best bet for completion)
The best way I can think of without significant modification is to have many different "layers" to the maps.
The surface and UG 1-4 layers would each contain their own sets of units, structures, and maybe even terrain. They would be loaded or unloaded depending on what level the player was controlling, or maybe even overlayed on top of each other if the player had a *hitload of RAM and wanted to view multiple levels at once.
Even an interior view could be achieved as its own layer. When loaded, it would replace each building/unit/tube with cutout versions of itself, and load a bunch of people-shaped "units" that would travel through the colony, "docking" with certain structures or areas of a structure depending on what task they were performing.
As I understand it, the OP3 Genesis maps are basically just points in space, connected by polygons. They are about the most flexible map format you could possibly have, and should be right at home rendering anything from landscape, to building interiors, to little people.
EDIT: Come to think of it, maybe we don't have to wait for OP3 to be
fully completed, the engine will probably be up and running long before the story, in which case maybe they can be convinced to let us borrow it, with the promise that we will use it only for good and not evil.