I'm not sure where the discussion of fitting in the box came from, but heh, I have never used the built-in storage method; it is horrible if you plan on mixing expansions. (I play games just like on Iso)
My current storage solution, for kicks and giggles:
The Base cards box holds all the basic stuff for 2 players, including Spoils, Ruins, etc. It's actually the perfect fit unless Guilds introduces something wacky. I have a separate bag containing the extra base cards needed for 3/4p. (I refuse to play 5/6, but have 2 extra sets elsewhere just in case anyway). I keep the Base Cards box, the Seaside made, counters, etc all in the Cornucopia box.
I use a program to randomize the order of ALL kingdom cards and sort them that order in the Dominion box. (no black divider thing). As we play, I move "played with" cards in the Seaside box until all have gotten love, then repeat the process going from one box to the other. Seems like a lot of steps, but in the end it really works. Granted I do not sleeve individual cards--I keep my cards separated in jewelry bags. I think Guilds will make it impossible to just use the real boxes though.