Now that I've had more of a chance to play, I've definitely noticed some improvements in the strategy Map AI. It uses Transports a lot more now. Still, though, I have seen it do some peculiar things.
In a Custom Campaign in Rivellon Heartlands, I've seen Karthan load transports, send them off the island, and then in the next turn, take them right back and unload them from where they started. I don't think I had changed the composition of my forces on Orcha. On the bright side, when he did choose to invade, he did coordinate and invaded with several transports at once.
The AI moves Transports about a lot more now, they still need to learn to escort them with Ironclads so they don't get shot down - in large part because they don't really build Ironclads, Juggernauts or air units on the strategy map.