I agree that the "Starting out Series" is excellent.
I also like the "Move by Move" series.
The "Move by Move" series in general cover a larger space of variations than "Starting Out" and are therefore thicker. There also seems to be more descriptive text, but do not have the nice graphic attention grabbers to important points that the "Starting Out" series has.
At a simpler level, a general survey book like Fine's "The Ideas Behind the Chess Openings" or Seirawan's "Winning Chess Openings" is a good thing to have.
You are correct to avoid opening books that are just a list of lines. Even those with good annotations like the "Grandmaster Repertoire" series, do not provide enough connection to the middle and endgame. If you find lots of lines terminating with "and white stands better" or "is equal" without more explaination, move on to another book.
IMO, opening encyclopedias are bad (MCO, ect). For master level players trying to explore new ground, they have been supplanted by databases (and long before that by Chess Informant). For the rest of us there is not enough explanation, not enough answers to why or why not.
Even the best opening book will have gaps. I have not found an opening book that explains why 3.Nf3 and not 3.Nc3 in the Slav. (The answer is that black can transpose to a problematic line for white of the QGA with 3...dxc4)