Prometheus Entry into the Moon's atmosphere...

If memory serves me correctly, that statement was made before an extensive tour of the planet. We don't see it (for reasons of pacing) but Ridley says on his commentary that the locating of the pyramids took place several hours after atmospheric entry. So, it's probably unlikely that said hard spots are anything to do with the Engineers. But you never know...

You are probably right,,as this moon seems to be devoid of life,,,in any form..except for what is related to our story. Sort of makes you wonder why the Engineers didn't select it for a terra forming experiment..

Even finding the pyramids after only a few hours of searching would seem unreasonable, especially given the mountaineous topography and opaque cloud distribution.

Perhaps Ridley should have just constructed a 168 hour long film of nothing but the Prometheus scouring LV 223 for signs of sentient life (rolls eyes).

With so much cloud cover it is a wonder thay found this right valley at all.. Maybe it was the only non storm area they could find!