Style Choice =/= Broken
All custom brick textures do with shaders is eliminate the light reflection off of texture parts that have positive white transparency. It doesn't break your shaders, or stop them from working. It merely reacts accordingly to the textures making everything less shiny: a visual effect that I, for one, despise.
Stop using the term "break".
Yes we all know you hate the plastic effect on plastic bricks.
But majority of the studs where based on the old stud texture Badspot used before shaders where implemented.
They where not supposed to make everything less shiny, they where supposed to be exactly like the default ones only their stud size increased by 125%, therefor they where and some still are "Broken", until they receive the proper transparency.
Just like you said you personally do not like the effect, that is your entitled opinion.
Zapk made his textures as a replacement for squideys so they work the way their supposed to like the default stud texture, you got me curious now though, I'm going to use your studs for a few days to see what difference it makes.