It's probably not even an issue of party. You have to remember that Silver works for a media outlet and the media needs a horse race when it comes to presidential elections. He's only doing what he needs to do for his employer to stay relevant.
My take on Nate S and 538 is that he started as this political geek in '08, made a big name for himself, shifted and got a raise and hired onto the NYT in time for the '12 election, and then got his dream job working for ESPN in time for '16 and focusing on sport statistics, which is his first geek love, and now has a decent job with people working for him, and doesn't pay as much attention to politics as he used to, since its only one of his business service lines, and the new bosses are a bit more interested in his sports stats than election stats.