Likewise, things that start off perpendicular with dot product zero, like the two basis factors, quite often don't stay perpendicular to each other after the transformation.
Then after that, I'm going to give you my take on dot products, and something pretty cool that happens when you view them under the light of linear transformations.
Ordinarily, the way you might think about one of a vector's coordinates tape its Z coordinate, would be to take its dot product with the 3rd standard basis factor, often called k hat.
So in that very special case, X would be the dot product of the 1st column with the output vector, and why would be the dot product of the 2nd column with the output vector?