I have been trying to change the fillstyle for the filledcurves option in gnuplot so that the fill colour represents the difference between the two curves on a 2-dimensional
Try to use filled histograms.
set style fill solid 1.0
plot \
datafile u 1:2:3 lt palette w boxes,\
datafile u 1:2:3 lt palette lw 2 w l
Column 3 defines color filling color according to palette settings, columns 1 and 2 define data points. You can also use background color histogram for clearing parts under graph.
I'd like to add image but I can't because of low reputation.