Redrobes, turns out Blender's boolean is actually quite clean. There's two solvers in the modifier, bmesh and carve...I got better results using carve, which only disrupted visible edges. I cut all the windows in one single operation and spent about ten minutes cleaning up errant vertices by snapping them to their most logical neighbor in the topology and running a remove duplicate vertices operation, which welds them cleanly.

Once I detach the exterior walls from the interior walls, I'll be doing some smart subdividing in order to get nice clean even spread of polygons to prevent long range culling issues, but I believe the engine handles culling pretty well...I'll definitely be discussing it with the Godot community for sure though. Thanks for the breakdown!

I didn't get as much time to work tonight as I would have liked, but here's an updated. I only really modeled one ward, but it was easy to duplicate it and get almost this whole end of the building.

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And in order to see the character of the building start to take shape, here's a duplicated wing section up.

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Once I add floors and ceilings, and of course the space between them, there'll be a bit more space between the levels vertically. Moving right along though!!!