Yeah, to be honest you're not really meant to be playing that far into the tech tree. We'll hopefully be replacing the X1 Shrike with an entirely new design for the Pegasus, and I'm still not sure exactly what we'll do with the Valkyrie.
You're still right that the Pegasus having 16 soldier carrying capacity is incorrect, though - it should be 12 like you say. I'll change that in the hotfix. Thanks.