I have just come across a fascinating piece, a lecture on Newton by Keynes, delivered posthumously by Keynes' brother and largely based on Newton's unpublished papers, apparently totaling about a million words. The central thesis is that Newton's "unscientific" work was just as careful and logical as his scientific work, that he approached alchemy and theology in the same way he approached physics and mathematics. In each case he was trying to make sense of the world by the power of his mind.
Which suggests an interesting idea for a fantasy–I don't know if it has been done. Suppose Newton was right in his exotic work as in his invention of modern physics. In one possible version he is still around, having discovered the alchemical secret of eternal life and faked his own death. In another, a modern scholar reads through the whole body of unpublished work, correctly works out the magical secrets that it contains and that he concealed, and makes use of them.
And in a third, alternate history, version, Newton's friends fail to pull him away from Cambridge into the conventional world of parliament, civil service, and society. He spends the second half of his life as he spent the first, produces breakthroughs in the Hermetic sciences as great as in the natural sciences, and history forks.