They obviously have a say in the game but its not on the same scale if they owned the company. Yerli has gone on record as saying the game didnt come out they way they thought it would, ai bugs were one of his main complaints that were supposodly buried deep in the code. Obviously it wasn't as open world as they wouyld have liked, probably to limitations of putting it on console, but that being said they already had 3 jungle based games before that, a change of scenery was welcome although it was very limiting.
As for the Prophet thing, its clearly his voice at the end of the game, not sure whats the story there but maybe cleared up in part 3.