Like you, I tend to think Rand will form an alliance and/or truce with Tuon, rather than ruling over the Seanchan. The trouble is that Rand offered a truce in TGS, which Tuon flatly refused. It could be that the Seanchan defeat at Tar Valon might weaken Tuon's bargaining position, but unless something else changes, I'm not sure why Tuon would accept an equal alliance or truce now when she didn't in TGS.