This is great for users, but it’s terrible for the SEO of those independent wikis as you’re telling Google you want to click on Fandom and Fextra links.

/edit

It appears this is no longer the case and the extension does things a lot better than it used to!

That might be true for the default config in the extension, but you can also configure the extension to de-emphasize fandom wikis or outright hide them in search results. I don't quite remember the exact default config though.