I don't have a direct source for this but my speculation based on the story is, that because he's
so fundamental to the end of the story, as he's the one that thought
he was protecting everyone by not explaining what he thinks he
understood about Hill House/Olivia and because of the sacrifice he
makes, I feel like the choice to have him be played by a different
actor, makes us feel the weight of time and how these things have
changed the character with the unspoken burden he put on his children by
concealing information and distancing himself from the family.
IMO Timothy Hutton makes one feel that weight, where Henry Thomas just seemed so much lighter, causal, and unburdened and I think that is the point. The Dudleys don't really change. They're characters that seemed to understand Hill House from the start of this story and are more secondary, informing the Crain's story and tying into the mythology of the house.
To help support my answer, the following interview with Mike Flanagan talks about the reason the story isn't just taking place in Hill House and why he chose to go that route, -what it does for the story, which matches with some of my speculation
Mike Flanagan Interview Snippets:
I was also really intrigued by exploring the aftermath of a haunting ―
typically, in horror stories, the unlucky victims of a haunting leave
the house, or exorcise the demon, and then the credits roll. I was
really fascinated by the question of what happened after, and how
someone would carry that trauma ― or even some of the ghosts
themselves ― with them into their lives.