There is a difference between setting the opacity for a contour map in the Properties window via the Layer tab and by setting the opacity of the fill colors in the Colormap dialog in Surfer.

Setting the opacity via the Layer tab will set the opacity for the entire contour map layer. This includes contour lines, contour labels, fill and hachures.

Setting the opacity of the fill color (clicking the Levels tab and clicking the Custom colormap (...) button in the Fill colors field) only affects the opacity of the actual foreground color fill. It does not affect the opacity of the contour lines, contour labels, or hachures.