I agree with the "pure-bred/well-bred" concept. I myself have two beautiful babies and one is pure-bred AND well-bred (from a very reputable breeder) and the other is pure-bred and not as well-bred (from a byb) but still has all of the traits and characteristics one would expect in a boxer.
My Princess, on the other hand, who went to the bridge in August, was a pure-bred but definitely not well-bred at all. She had several of the characteristics that you have described with Tyson. She was skinny and had much longer legs than most boxers and her head did not "stack" ( it was not square and box-like) but there was no doubt she was all boxer. Every character trait she had (ie kidney beaning, the woo-woo song, being extremely rambunctious, etc) was exactly how a boxer would act, she just didnt look quite right. Nevertheless, she was my beautiful baby and I wouldnt have traded her for a "well-bred" boxer for anything in the world.
Bottom line to me is this, unless your a breeder (and by breeder I mean someone who breeds boxers for quality and conformation not quantity and money) wether your boxer is well-bred or not shouldnt really matter too much. I know from experience that a non-well-bred boxer has a higher chance of health problems and they might not look quite the way we expect them to but they still make the most wonderful pets in the world.