Could the pyramids be the default color until a player actually visits it (don't color until surface exists), and the color it appropriately, with an additional color (darker?) to show it's been looted? Maybe an option under Map Settings that can swap between configurations?

a looted pyramid reverts to the normal grey color.

versions above 1.0.8 are aimed at showing the pyramid colors in the universe explorer, and for those to be accurate the mod is forced to scan the planet and generate the surface (which it cannot cleanly delete afterwards, space exploration api lacks it), if you wish to avoid it you can downgrade to 1.0.8 just fine.