It was probably by Kojima's direction since Snake is modeled after Pliskin anyways.
And I don't get this hate over Hayter adjusting Snakes voice over the years. It seems obvious that he was trying to reflect how the years were affecting Snake. Aging and smoking for years will fuck your voice up. I mean if you don't like it fine, opinions and all that, but it's not like he was performing badly or losing a handle on the role. It was a specific creative choice. And being an actor means nothing for VO. Plenty of actors are awful at it.
That being said, I'm not upset about the change. I just don't see the hate for Hayter's performances.