That is already part of the retconned premise. When we hear that the Mark is killing us at the start of the story, we are led to believe it's the Breach that causes this, and it's never even hinted that Solas controls it on a continuing basis. Given the situation at the end, it's plausible that he could control it, but it doesn't necessarily follow that he did. Thus, the setup at the ending is not an unavoidable implication of anything that occurred earlier. You wouldn't need any extra contrivance to set things up differently for the end.
We were led to believe that closing the Breach fixed it by Solas. We were also led to believe that he didn't know what it was. There is no retcon here. We didn't have all the information, and now we do. No contrivance necessary, and frankly, I'd tend to believe that this was the intended path from the start. Giving us clues to Solas manipulating the Mark after Haven would be a spoiler to the rest of the story.
I did not contest that. It is plausible. However, I contest that anything that happens necessarily causes our alternatives to be restricted to "serve the Chantry or disband". For instance, if not complete independence, we could've chosen to ally with one of the other present powers.
No, they wouldn't have to. See above.
How is Ferelden going to react to you banding with Orlais, especially since you control a couple of keeps in Ferelden. Given the history of the region, do you think they're going to be happy with that? They want you disbanded, for a reason: You are a power unto yourself, but you are established as such within their borders. Do you honestly believe BW could sell "...and the Inquisition allies itself with Orlais, and we all live happily ever after"? First they have to rewrite the war between Orlais and Ferelden, to remove any concerns of Orlais planning a coup to take back what Ferelden just took back. Then they have to rewrite Ferelden's reaction to a major power taking control of keeps in their territory, which can be tied directly to what just happened with Orlais in the timeline, where they have just, more or less recently, been kicked out of Ferelden, and now there's another major player establishing itself within their borders. They want it disbanded, tying it to the Chantry is of benefit to Ferelden too, since the Chantry serves, or rules them as well.
That's a lot of changes just so they can leave the Inquisition alone, but then it's even more messed up, because Orlais wants you leashed to them. All that stuff I wrote about Ferelden above? Apply it here as well, only we only control one keep in Orlais, along a major trading route. You see, if we were on some island some where, with no influence other than through political ties, it would be ok, but we're not, and trying to establish us as being so now, with Skyhold being said island, means they have to change a lot of stuff that actually happened in the game.
As the world is now, at the end of Inquisition, not the end of Trespasser, allying with Orlais or Ferelden would be bad, but thumbing your nose at all three, including the Chantry here, could be much worse. It should lead to yet another war against a despot trying to be a God, the Inquisitor. If Orlais and Ferelden bring enough pressure to bear on the new Divine, she will eventually have to cave, or face a war against both of them. The absolute best outcomes for the Inquisition are written into Trespasser. Those that want to keep it can ally it with the Chantry, which will quell a lot of the objections from both sides. Disbanding it can be the ultimate nose thumbing at everyone, except Ferelden, who gets what they want, because all the ties that you've made over the course of the game become yours, and yours alone.