Presumably because the new project, unlike anything else in the intervening years, is "good enough" for him to feel satisfied with it.
In my previous answer, I dug up several quotes from Bill Watterson showing that he always said he never wanted to write for the sake of writing, or for the sake of money, but to produce something that he felt was valuable and worthwhile. As he said in 2013:
Well, coming at a new work requires a certain amount of patience and energy, and there’s always the risk of disappointment. You can’t really blame people for preferring more of what they already know and like. The trade-off, of course, is that predictability is boring. Repetition is the death of magic.
He never totally ruled out doing new projects, but he made clear that it would need to be something he considered worth doing, something that would require a big investment of time and energy. And, according to the publisher of The Mysteries:
For the book's illustrations, Watterson and caricaturist John Kascht worked together for several years in unusually close collaboration. Both artists abandoned their past ways of working, inventing images together that neither could anticipate—a mysterious process in its own right.
That sounds like something worth coming out of retirement for: not only a new project, but a new type of project, requiring new inventiveness and ideas. Working with John Kascht, "regarded as one of America's most important and highly regarded caricature artists" (same source), would presumably also be a plus.