Chuck, I'm with you on not having the legs go right through the top. My reason is that the top wood will move more than the leg wood, because the grains will be running 90º to each other. So you might end up with a leg either protruding very slightly or receding very slightly from the top surface of the table.
Unless you want an arts and crafts type appearance to the top, then in that case you could deliberately have the legs protrude 1/4" or so.
As for the top construction, I think I would be inclined to go for a box type setup as suggested by Señor Stick. That helps keep the table flat and you can use considerably thinner wood for the top without it being obvious.
OK, fess up...which one of you clowns stole my sig? It was right here a second ago.