these cups look too "flat" on their base ..

Do you know what kind of stone is it LS? Looks a bit sarseny in some of those pics. In which case I'd be tempted to go for the old 'mangrove root indentation' explanation. But the flatness of the inside of that ring looks artificial. Romans maybe? They were a strange bunch, who knows what they may have done to other people's special stones.

Welcome to the joy of prehistoric rock art. The level of uncertainty is a crucial part of the fun ;)

Either way, artificial or not, one can always feel comforted by the thought that holey stones were special, and so the presence of such can be taken as an indicator of possible prehistoric significance, especially so in an area generally devoid of such things.