I'll answer some of your points raised, leaving the rest to be answered by folks with more specific experience.
Ejecting the Reader is fine, you can forget about the Setting altogether.
Regarding your UNREAD books, you can easily delete a book after reading it from that collection directly.
Epub books work very well with Sonys, PDF's ... okay, but not as well, with a loss of formatting other than the default Small size. Far from a deal breaker for me.