As I understand the Altar of the Lunnotar is connected to the The One via association. I believe the Lunnotar is also connected to the Altar somehow, though it could very well be that those in possession Altar can recognize the significance of the Altar without previous knowledge of the One (or without the aid of the Lunnotar). The way I see it, those in possession of the Altar would probably only recognize the fact that its soaked with holiness. Only latter on when they have renovated it do they realize its true nature. I suspect that when fully or nearly "repaired" that even the most mundane people can just glean its significance by looking at it. I imagine that The One's aura was so uber that his mere presence left an unmeasurable influence that those in control of the alter can hone in on. Leaving them with a compass to the True heaven.
Of course this is all conjecture...
Edit: Oh and as far as the Tower of Mastery is concerned, I believe it to be a controller of sorts that allows one to manipulate Erebus as if one had the power of creation, as apposed drawing up magic from the nearly infinite elemental vaults that a certain fallen angel made. This would be rather remarkable if true, as I believe that none of the angels have ever manged to make anything from scratch since The One took the power away, perhaps I'm just an humanist but I would like to think that.
