Fill Rectangle only has an effect if you have chosen Equal Aspect axes. Imagine that you have asked FX Graph to draw Equal Aspect axes and you want both the x and y axis to go from -10 to 10. This will produce a "square" set of axes.
If you are using this set of axes in a normal FX Graph window, FX Graph must add white space to each side of the graph to keep this square shape.
If you turn Fill Rectangle on, FX Graph will fill the sides with more of the axes - it uses your -10 to 10 settings as a MINIMUM requirement. The axes are still equal aspect but you do not have this wasted space at the side.