Color surface can be drawn at the base or top (then it is a gray/color planar map) or at z-coordinates of surface points (gray/color surface). This is defined by the `at` option with a string of up to 6 combinations of `b`, `t` and `s`. For instance, `at b` plots at bottom only, `at st` plots firstly surface and then top map, while `at bstbst` will never by seriously used.
Colored quadrangles are plotted one after another. When plotting surfaces (`at s`), the later quadrangles overlap (overdraw) the previous ones. (Gnuplot is not virtual reality tool to calculate intersections of filled polygon meshes.) You may try to switch between `scansforward` and `scansbackward` to force the first scan of the data to be plotted first or last. The default is `scansautomatic` where gnuplot makes a guess about scans order. On the other hand, the `depthorder` option completely reorders the quadrangles. The rendering is performed after a depth sorting, which allows to visualize even complicated surfaces; see `pm3d depthorder` for more details.