I'm all for reading between the lines.
Primal's line in Bad Spark - "somewhere far, someplace barren". As you said, why would they give the Stasis pod engines? You can draw the conclusion that it was a specialised pod for holding him. We know it's true because it's bigger than a normal stasis pod. Its a temporary prison at best. They knew he'd break out of it, but as long as he was somewhere he couldn't cause any trouble when he did, then all was well.