i think in some cases the reckless breeding practices of the BYBer brings older genes to the forefront. for example danes, almost the only place i've seen the broad chested blockheaded tight skinned original working style of dane is BYBs. most well bred american danes are too narrow chested w/ rectangular heads that are less efficient for the breeds original function. most european stock looks like a mix of english & show quality neo mastiffs and is too heavy for the running involved in actual hunting.
BYBs breed anything w/ papers (sometimes not even that) so alot of older genes that are suppressed in "good" breeding programs get expressed by BYBs. honestly i hate to say it, but i'm okay w/ that to a degree.