Rabbi Kaplan took a shitah in a kabbalah sefer that he admits the Arizal said was a base error, and decided that for the sake of Kiruv he can (a) decide that it’s correct, and (b) interpret it in a way that fits in with what some people who cannot accept the Torah believe. He based this strange methodology on his erroneous interpretation of a Rambam which he believed allowed him to basically say anything is correct if he finds it somewhere in a sefer, even if we know its a mistake, simply because it’s a hashkafa issue. I know that doesnt sound coherent, and its not, but thats basically the position.
But at the end of the day, his conclusion in that essay – that the world is billions of years old – has been declared by Rav Elyashev, Rav Chaim Kanievsky, as well as the rest of the Gedolei HaDor to be simple kefirah. He meant well, and Hashem yislach lo.