A studio that decides to add their own personal touch to a Bible film is like any group that decides to create their own adaptation to any published work. There are bound to be some differences between the overall book and what the studio creates. This does not mean a studio shouldn't be allowed to have some creativity when creating their adaption, but any changes they make should be in good taste and for a reason. However some changes are better suited for certain Bible stories.
If a studio is trying to focus on the life of Jesus and wants to deviate from the story by taking out one or two of the apostles — or merging them into one character — it might not be a good idea to try and combine major characters like Thomas and Peter, or in a “twist” have John be the one who really betrayed Jesus while trying to make Judas Iscariot look like a hero. While some stories do well with having the bad guys come out looking like antiheroes, this would disrupt the overall meaning of Jesus' death and really tick off some viewers.
An instance where this might work would be the story of Noah's Ark. There is no way a studio can get every animal on the arc. Leaving a few species might be okay. The meaning and the story of Noah's arc is still intact. I'm sure a studio version of Paul the Apostle could benefit from some studio treatment.