Staring at the two ruin layouts for a bit I've come to a conclusion; the layout and position of everything, even the artifacts must have meaning, or else why would FD take the time to reorient them?
Instead of this brute force tactic, i think we should focus on what possible meanings these positions could have.
Also, note the beacons did not move thus probably are licational, as FD never moved them, only changed the order we would be directed to find them.
I agree with your idea that the changes could be important, but woult point out the beacons did move (several). Also the items, also many of the obelisks.