The pickup cavities are not the same. They are usually smaller on non-pickguard guitars because you have to leave enough material to get a good bite from the mounting ring screws. Or if you have
direct mounted pickups they are even smaller and more "form fitting" to the pickups baseplate. Pickguard routs are looser to allow for play in the pickguard placement, and simply because they can be. As you pointed out, the guard covers all! Some fenders routed a huge "swimming pool" rectangle under there.
As far as matching the look, I would say get a clear guard (smoked or tinted looks cool, too) and epoxy the same species of wood veneer up underneath it. You'd be able to tell it was a different piece of wood because the grain wouldn't line up, but who cares?