What a long winded intro - but that's not a bad thing! Welcome to the board.
FYSA (which you may know) the second Magus card is just one of the versions Frieda went through before they settled on the final Magus. The cards are printed on boards of 4 and to fill up the board, they printed the extra Magus design.
Btw, I love the Thoth deck to. I first ran into it when I was 16/17, a couple of years before I got into Crowley but was fascinated by the beautiful designs. I still think it is the most beautiful deck out there and the most "magical".