FBReader is totally customizable. Note that this includes ignoring some (most) CSS in favor of user-specified layout options. For ePubs, it also does not display most SVG graphics and tables. Even so, it is my favorite ebook reading app. See the attached screenshot.
The B&N Windows app has customizable colors, and displays ePubs. It also ignores some CSS, and I'm not sure how it does on generic ePubs (vs ePubs from B&N).
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