Because the Gaussian surface we chose was a sphere concentric with the point charge, the electric field and the area vector were always in the same direction giving an angle of zero degrees in the dot product.
Since we just saw that this change vector has a constant magnitude, the only way for this dot product to stay the same is if the angle it makes with that collision line stays the same.
E.g. you could have two vectors, generally pointing in the same direction with a positive dot product, which get pulled apart from each other during the transformation, in such a way that they end up having a negative dot product.
For example, you could have two vectors generally pointing in the same direction, with a positive dot product, which get pulled away from each other during the transformation, in such a way that they then have a negative dot product.
So, in that very special case, x would be the dot product of the first column with the output vector, and y would be the dot product of the second column with the output vector.
Alright, so look back at this conservation of momentum expression, telling us that the dot product between this square-roots-of-the-masses vector with our change vector is the same before and after the collision.
Likewise, if things start off perpendicular, with dot product zero, like the two basis vectors, there's no guarantee that they will stay perpendicular after the transformation, preserving that zero dot product.
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.