That extension looks to be a complete restyle of HN, which is probably why it was not interacting well with Dark Reader. I don't know what features you're looking for in the extension, but there's another called Refine Hacker News which adds features but doesn't change the styling. It does work well with Dark Reader.
I love Dark Reader but have it disabled on HN.
I use "Hacker News Readable Dark" under Stylus and this site looks fantastic.
Edit: I just remembered I've been using an extension called "Hacker News Enhancement Suite" to enhance the layout of HN, and after disabling it, Dark Reader worked so I think that extension was somehow interfering with Dark Reader.