I have opened 2 1999 Topps Factory Sets. (the blue box and the series 1 and 2 retail set boxes)
Both sets yielded the same 10 cards mentioned above with the backs reversed from the rest of the set. 1 (Clemens), 13, 34 (Ryan), 62 (Vlad), 84, 85 (Jeter), 95 (Pedro), 96, 143, 174.
The factory set came in a 3rd flavor, a white box with a bonus Ryan Finest Reprint bonus card (referred to as the Christmas factory set). I will see if that factory set is any different.
I don't have alot of 1999 Topps cards from packs, but the backs match the direction in their factory set counterparts.
If the 3rd set is exactly the same, I feel like there is likely no difference between factory set and pack card backs.