I think you are misinterpreting Rand's thoughts in that chapter. He came there to destroy the Seanchan, convincing himself they were monsters. He needed to believe that to do the final act. Instead he found they were not monsters. They don't abuse people as long as they obey their rule, and in exchange give them stability, order and security - and food. He still sees their horrible treatment of channelers, but he now views them as people with misguided beliefs rather than evil. This led to his inability to destroy them - not to any decision to obey them.
The Seanchan prophecies don't say that he'll bow to the Crystal Throne. They go much further than that. They say he will "kneel" to the Throne, and will serve the Empire by fighting the DO "for the glory of the Empress".
I don't see how the above can be a true prophecy, nor do I see Rand becoming a mere servant of the Empress - can you?

The Crystal Throne is an evil ter'angreal that induces compulsion. I believe that we'll see it destroyed in one of the upcoming books - this will be part of the proof that the Seanchan prophecies are corrupted and maybe help convert the Seanchan monarchy to a less oppressive regime. All high and mighty rulers in this series end up being taken down many pegs. It's even part of the prophecies. The Seanchan will get their comeuppance, and I for one, am looking forward to reading it.


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