Logically Magician should try to appreciate, how the art work done by any software package looks like.
Whether it is top layer or bottom layer, they are looked as if from top. now for toner transfer method of PCBmaking, the paper pront shoul be also viewed as if from top. as it is not possible, one has to print a mirror image, and when the paper is placed with the printed part placing downwards, it will register correctly.
but the bottom layer can be printed as it is , as we are already looking at a mirror image. as the paper is paced on the copper clad it just works.