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Whats the difference

Neck-throughs also are less prone to having dead-spots.

They will sound will be basically the same, because a big part of the Thumb's signature sound comes from the wood type, the pickups locations and the elctronics, more than the type of neck construction.
 
The NT has a 3 band EQ, the BO has a two band EQ. The body of the NT is smaller (probably down to weight considerations). The woods are different, the sound have similar characteristics, but the NT sounds more refined and even to my ears. In any case, I loved my BO, except for the ergonomics (heavy, balance issues). It was Wenge neck, and I found it sounded different from the new models too (less woody tones, more bite, monster growl, and was one mean metal machine).