If I had to choose between one or the other, I'd go with the 2012 remaster. None of the bonus tracks on the twofer are earth shattering. The stereo version of Smiley Smile is fantastic and makes for a great listening experience.
Just go to youtube and listen to the twofer bonus tracks and see if they are anything that you must have.
I'm pretty sure all the rest is on there, but as far as "Can't Wait Too Long" and "Their Hearts Were Full Of Spring", I don't think those appear elsewhere in those versions. The version of "Can't Wait Too Long" on
Smiley Smile/Wild Honey is over five minutes long whereas the version on the 1993 box set is less than four minutes long. And then "Their Hearts Were Full Of Spring", I don't think the 1967 version of that is available anywhere else.