The reason the left and right side fins are slightly offset from center is the fins are flat on the inside (not symmetrical) and the jig automatically offsets the fin placement to line the flat inside surface with your shaper's dots.
Although that's just standard industry practice to offset the fins like that, no one will ever know if the board surfs better with the fins 1/8" over here or 1/8" over there... it really doesn't matter...
The jig is marked with a "right" and "left" side.
Looking at the bottom of the board, place the "right" side jig line on the dots on the right side of the board. Vicea-versa for the left side.
Center fin is pf course on the center line.
More info can be found in the FCS II install guide.