This is just a theory about current archon stones but....

[Yowyow]

Can a Mod respond fast if this is breaching NDA, it might be. But lets get on with the juicy speculation... Althyk the Keeper, http://ffxiv.gamerescape.com/wiki/Althyk
Does any1 think his allagan stone location north of Nine Ivies during Living on a Prayer might possibly be the current location of the Sanctum of the Twelve cathedral? It has been bugging me since the pictures we seen posted of the cathedral on a blog post. It also makes me wonder if Althyk himself or another archon is the demon / Sucubbus seen fighting in this blogpost http://na.finalfantasyxiv.com/blog/post/191
If so... That raises an eyebrow and a few questions about how Tanaka invisioned 14 and how Yoshi invisioned 14. Both of them knew that somehow, someway this would be the future of the Archons. Like i said its PURE SPECULATION. But has me and a buddy asking a few questions. Discuss!

[Enkidoh]

I don't think this is in breach of NDA, not unless you directly reveal/discuss something that SE hasn't already mentioned or revealed. So anyway...

I doubt the Cathedral replaces that Deity Stone - as when the Cathedral was first announced in the Blog it was mentioned that the cathedral had 'always been there', it was just abandoned, forgotten and overgrown by the Twelveswood.

It was only with the damage to the Black Shroud caused by Dalamud's Fall was the overgrown cathedral finally revealed, and was then repaired and restored to it's original glory in preparation for wedding ceremonies to be conducted there. I'll try finding that information on the Blog and post what was said about it here.

EDIT: I went searching through the official blog/main site and couldn't find any mention about the cathedral, which is odd, as I distinctly remember Yoshi-P talking about it in regards to wedding ceremonies, and that he revealed a bit of the lore behind it.

Ah well, until I can find more proof, take what I mentioned with a grain of salt (a la, fan theory but not proven).