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When you download an epub3 from Standard Ebooks the file extension on it is .epub3 so you need to delete that 3 so that it's .epub. You may need to tweak your Windows settings so that it shows you the file extensions (always a good idea in my opinion).

I don't know what the epub standard says but it wouldn't surprise me if the extension is supposed to be epub and not epub3.

Internally it's still an epub3 and the kobo will recognize it as such. I doubt if there's any advantage of downloading the epub3 over the epub2; I used to download the epub3 versions but now just get their epub2s. Somewhere I'd downloaded a book that had @ lines at the top of the css which caused my kobo to ignore all of the css; dunno if it was Standard Ebooks or somewhere else.