The first one would be possible with a lot of time on their side, but unfortunately they don't have that much time. There's also the tricky fact that the instant they separate them, the UE AI will launch an attack in the present.

The second option would lead to the UE AI becoming aware of its Transport AI hijacker, and immediately focusing all energy against it. And, unfortunately, the UE AI is far more advanced than our dinky little hundreds-of-years-earlier model Transport AI. So without drastic countermeasures (still possible), the UE AI would overtake the Transport AI in Exsilium, rather than vice versa.