I say mostly because units can actually move to be above and below each other, but only certain units can fly through debri that usually conveniently makes a maze in space. That's right, you can create fences. Walls and fences would block opponents from coming into bases on a planet. It really defeats the point of having a strategy game in space and really seems to defeat the purpose of using a 3D engine. Which is perchance one of the most annoying things in the game.
Units can pile on top of each other and travel over and under structures.
But unfortunately, they forgot to include this option with structures being able to pass over one another. Well, one of the better ideas in the game also introduced this problem. One of the vehicles that you can build in the game is a towship. They can attach a line to any structure and tow it around like a tugboat. And while this is cool so you can move your defenses around after you've built them in order to move defenses forward quickly and the like, you also have to tow large structures into certain locations to complete a mission.