It isn’t merely a contemporaneous difference. His views haven’t changed on these topics. His work on the the Church–Turing–Deutsch principle was published in 1985. Compare with these comments from a 2010 interview.

Drawing on the material in Fabric, he observes that all the fundamental explanations discovered thus far have explanatory gaps. A “theory of everything” (of which Fabric might be considered prototypical) is inter-theoretic: The explanations rely on each other to fill in the explanatory gaps. In other words, he wholly rejects reductionistic accounts. One of his most striking examples is referenced in the article, “how do you explain the presence of a particular copper atom at the tip of the nose of the statue of Churchill in Parliament Square?”

This is an important difference: “You could say that any one of the four is emergent with respect to the other three. You could regard any one of them as being the basis of everything. Indeed, in all four cases there are people who insist that this particular strand is the real underlying truth and that the others are built on top of it. For instance Stephen Wolfram is one of those who believe that the computational strand alone is the real underlying truth.”

His other concern: “You might think since I’m so keen on unifying computation with physics that I would be keen on Wolfram’s idea but I’m not. There are two reasons. One of them is simply that his type of computation is classical not quantum, and I think it’s a great mistake to think that there is anything fundamental about classical computation…I think the relationship is entirely the other way around: which operations we can and cannot perform, such as computations, depends on what the laws of physics are.”