First of all, how do you know the first trailer was timed to the cinematographer's intent but not the second? Or either? Trailers are usually timed by marketing departments under the control of the studio.
Second, what I see is that someone decided that this lava effect on this alien planet should be green instead of orange, presumably to make it more alien and mysterious since it somehow transforms the astronauts into the Fantastic Four, so that's more of a design issue regarding the effects based on addressing some story issue. It only sucks for the cinematographer who was told to light the green screen elements for orange lava only to see it changed to green, but that's hardly a big artistic statement by the cinematographer that was changed by the studio.
I don't see anything from that page you linked to that says that the whole color palette of the movie was changed in post, what I see is that all the alien lava / mysterious energy effects were changed from orange to green.
I will say that in a multi-million dollar movie, there are a lot of cooks in the kitchen and a lot of people who have a say in how the movie looks.