Not only is Christopher McQuarrie simply a talented writer, but because he’s worked with Tom Cruise so many times before, he knows how to use the script to play to the actor’s strengths.
It also makes all the sense in the world that if it’s going to happen, Tom Cruise would want to bring in somebody that he’s worked with before.
Bringing in a fresh set of eyeballs to look at a script and make some minor changes is a more common practice than you might realize.
This shouldn’t be read as anything other than business as usual.