Difference between top pad master and top solder mask gerber files?
In ancient times when PC boards were layed out using sticky tape and Bishop Graphics pad patterns on mylar film, you would make a pad master showing all pads, and that mylar would apply to both sides of the board.  The single pad master ensured that the pads on both sides of the board would line up.  You would make separate mylars for top and bottom side copper tracks (but no pads).

Later, red and blue tape for tracks were used, with black pads - then a single mylar sheet could be used for both sides of the board - the separate pad master was no longer required.  Photographic tricks were used to produce the top and bottom artwork, so the red tracks would only show on one layer, and the blue tracks on the other.  The black pads would show on both layers.

Now, with surface mount parts on both sides, and multi-layer boards, a pad master would be useless, as you need different pad patterns for each layer.