I think the details of any report or rumor are always going to be a little off. We're getting whisper down the lane, so even something that was exactly right to start will get distorted some by the time it shows up here or on another site.
But if we step back and take a look at the 30,000 foot view, I think we can examine the totality of everything we've seen from all sources and get a general picture of how things may have played out:
1. Leading up to the production of this film, Fox was still trying to get something from Marvel in return for the rights. That was their Plan A and actually making a film was their Plan B.
2. Because they weren't completely committed to actually making the film, they took half-measures. They hired a young director who had made a good film on a shoestring already for them and likely had contractual obligations to make another film if Fox wanted. Because he was young, Fox figured they could string him along as they got their s*** together. They also figured they could keep him in-line and doing their bidding if/when the project really started moving. They chose a 'grounded' script that would allow them to make the film relatively inexpensively if they had to go to Plan B.
3. When Marvel offered nothing and Fox had no choice but to go with Plan B, they realized they weren't really in love with their script or their director. He was more stubborn and difficult to control than they anticipated, and he had more ambition for a film for which low-cost was key than sat well with management.
4. They looked for replacements, but couldn't find anybody willing to wade into that swamp at such a late date. They needed to get started to meet contractual deadlines, so they charged ahead.
5. They sent Simon Kinberg to babysit Trank and keep him in line and on budget, but Trank rebelled against such an insulting move and soon he and management were at odds.
6. Again, because of contractual deadlines and investments that had already been made and because sets were already under construction and participants had dates locked into their schedules, they charged through with filming even though things weren't going smoothly.
7. With a combination of Trank, Kinbeg, second unit directors etc., they managed to get enough on film to move to post-production.
8. As they identified some of the most glaring short-comings in the film, they worked to fix those in post production and did some re-shoots to fill the biggest holes.
9. Trank and Fox also realized that their original plans for people and software for CGI weren't sufficient to get the job done and they looked for alternatives who could jump in quickly and fix things.
10. At this point, Fox and Trank probably don't think much of each other and will probably never work together again. But they have a film to release in 5 months and it's in their mutual benefit to hold their noses and get it done and pretend they're one big happy family as they do that.
I think the interviews over the next few months leading up to release will be interesting, and we'll see Trank and Kinberg squirming and being uncomfortable when they're not outright avoiding the press, but they'll present a general air of cooperation and happiness with how the film came out.
We probably won't get the real story for another 5 years or more, but that will be interesting when it does comes out.