There's no conflating. Scientism-types being atheist (or anti-theist) seems to be a pretty universal pattern in my experience. If I called someone a bible-basher, it wouldn't be conflating to say they're a Christian - it's a prerequisite. It's also a stereotype, but if I were to call somebody a bible-basher you'd (presumably) know the kinds of character traits I was implying (sanctimonious, primarily).
But this feels like describing the colour blue - if you don't already know what it is, being on Hacker News, I don't think I can help you. Familiarising yourself with the philosophy of science (like Karl Popper's ideas for a start) and then looking at the way that many redditors and HNers talk about science (especially pop-science in astronomy and physics) or treat whitepapers, "new study finds" journalism etc would make you notice the difference.