Louisoix admits in 'Living on a Prayer' that it was his Circle of Knowing that recently carved the symbols of The Twelve into the old stones around Eorzea and that they were to be used as conduits to channel the prayers. That's why they didn't glow, at first.
Ah man, this is why I hate speeding through quests lol. I totally missed this part. That changes everything in my theory. Thanks for the clarification. So many questions, makes me want to view every single CS and read every bit of npc dialogue.