Autobed leveling doesn't compensate
I believe that the matrix is shown transposed from how it should be, but that doesn't affect the answer. The compensated Z position is derived from the original (X,Y,Z) position by multiplying the corresponding vector with that matrix. This means that the new Z position would be

Z' = 0.999992Z - 0.001233X - 0.003905Y


If you have a 200 x 200 printbed, a diagonal move from one corner to the other would correspond to a 1mm change in Z-height. This should be noticeable, but if perhaps you're printing something quite small you might not notice it.

Though, if your first layer is perfect, I would see no reason to mess with it.