I wouldn't say there is such a huge overlap of alt-right and atheism. Certainly the "new atheists" like Harris skirt the line with their "intellectual dark web," but I would hesitate to call Harris or everyone who follows him alt-right. That just goes back to labeling everyone you don't like/don't agree with. From what I've seen the alt-right and the ethno nationalists (where I do think there is a big overlap) pine and wax nostalgic for judeo christian values. They glorify things like the crusades, when the noble European took arms against the great Muslim scourge. While someone like Richard Dawkins might find church bells less frightening than "allahu akbar," traditionally he and other atheist figures had much criticism for all religions alike, if anything, the most for Christianity as it impacts the lives of these people the most. This is messy, but what I am trying to say is it's not intrinsically atheist to be super sympathetic and defensive over Christianity.
I would wager that there is a good mix of atheists and Christians that make up the alt-right. I will grant that there is a greater ratio of atheists compared to the general population, but that is because they are mostly young people. I would think younger leftists are mostly atheist as well. If anything the left, historically, is much more associated with atheism than the right is (think USSR, Mao, etc.) And lastly, to use a silly anecdotal example, GAF was very atheist-leaning, and I presume Era is as well. Now that GAF took a hard turn to the right, the Christianity thread is now more active than ever.
So now, I don't think there is some direct connection between atheism and the alt-right, Himu. Maybe there are some gray areas where they intersect. But I think we've done a poor job of defining what is alt-right. It seems like a catch-all term. Like, would you say Etiolate was alt-right? Or an alt-right sympathizer? On Era they would certainly call Etiolate alt-right. They'd probably call this whole forum alt-right. There's levels to this shit.