I've had that issue before and I came to the conclusion is that there isn't a single good comic/book reader out there.
Here's my setup:
>CDisplayEX for comics
>SumatraPDF for EPUBs
>Evince for PDFs
CDisplayEX doesn't support EPUB and its PDF viewer is garbage, it's very buggy and it won't render the text at a higher resolution if you zoom it in, it'll take the text and resample it leading to shitty blurry text. For comics it works just fine and it can take .zip and .rar files with sequentially named images such as the ones you find on exhentai zips, it can resample things with lanczos and it's the only comic viewer for windows that does it so if you're not "reading" your doujins at the native resolution it gives you the best image quality.
SumatraPDF has the issue I'll talk about further down below, but otherwise its EPUB reader lets you set a background and text color flawlessly.
Evince reads PDFs just fine, and if you press CTRL + I it'll set the background to black and the text to white. The only issue is that while the pages may be black the blank space on the interface itself will still be a bright grey which is awful but there's nothing better.
Another thing, CDisplayEX in general is unstable and loves to crash, at least it remembers the page you were at unlike SumatraPDF however. CDisplayEX also won't let you read your images while it loads them which is really stupid, you have to wait a few seconds until it loads all of the 400 images on some overly long doujin before you can start it, which can take a minute.
>>9801
If you read a PDF with sumatraPDF and set the background color it also inverts the color of the images for some reason, and then you have to manually set it to white and black back and forth on the config file to fix it, I wouldn't mind that if there was a hotkey but there isn't.