There's no question that there is some considerable overlap, particularly with the first four albums which I think are the band's best. I'm not going into every last little detail but suffice it to say that the best tracks (or versions of them) from the four are well represented on the first two albums. However, the remastered editions of these albums contain, obviously, all the original tracks plus a number of live/alternate cuts and b-sides which are often different from those on the box set. CD3 of the set covers highlights of the successive studio albums. CD4 is a superb collection of live cuts.
Now while the remasters have new liner notes by Max Bell, the box set has a substantial booklet.
There are pros and cons about which to go for. For someone who just wants one collection of E&TB, and although there are several best of's, I'd recommended this lavish box set. But it doesn't tell the full story. Ian McCulloch used to rant on about Ocean Rain being the best rock album ever. He's wrong, of course, but not that far wrong and it should be in every rock fan's collection. Buy the box set and you miss a number of great songs and the same can be said of the first three albums.
I recommend you do what I did. Buy the box set (which, at its current price, is a bargain), revel in it for a while, and then go back and buy the remastered extended versions of the first four albums, plus maybe a later live set for a bit variation. But whatever you do, even if it's just buying Ocean Rain, you win.