BTW, I don't understand the use case of reading ebooks on a desktop or laptop instead of on a phone or tablet (or eink reader.) Is this really common? I can imagine reading some technical ebook at my computer while working at my desk, but not fiction or anything else.
Unfortunately, not everyone has all the screens, and not all phone screens are big enough to read novels and such. I'd rather read a book in my bed on my laptop screen and take notes quickly rather than an older phone and try to write on its keyboard.
Also, e-ink readers' screen refresh rate prevents taking extensive notes on the books. You can underline just fine, but longer notes are a bit hard.
Last but not the least, comic books in CBZ/CBR format really begs for a quality color display, since colored comics is half the fun in the comics. :D
Calibre doesn't obfuscate / embed the book files. They copy under a folder with Author's name. You can pretty easily access the original file pretty quickly. Maybe you can configure Calibre to use your directory structure without modifying it.