I see this issue: books rendering better when bought from the device mnfg. store, i.e. B & N, Kobo. If I buy a book from B&N and read it on a Kobo reader (or vice versa) I don't always have the same functionality. I may not be able to change the font style, margins, line spacing etc. In some cases I may be able to change a font style but not the margins etc.
Although this hasn't discouraged me from side-loading books, for the most part its been a minor inconvinence as opposed to a major distraction.