It bears remembering that when the Consolat were building up all this metaphysical 'architecture' that formed a giant reality-warping engine, they had every reason to expect to be able to go on working on the project, and no reason to expect any other race capable of doing anything with the project's apparatus to arise for millennia if not even longer ages.
When we think of a car, we take for granted that a car will have a keyed ignition. That you cannot even turn the car on without a little piece of metal that "belongs" to you and that specifically matches that unique vehicle.
But imagine a world where only one prototype car existed, and where the idea of anyone even thinking of stealing a car, let alone being able to drive it if they did, was unthinkable. Why not build the only car in the world with no locks on the doors, except perhaps a safety latch to keep you from falling out while the thing's in motion? Why not build the ignition to start with the simple push of a button?
Maybe the Consolat system was not designed to be 'picky' about who it works for, the Consolat simply took for granted that, at least for their 'now,' no one other than Animus would exist in the entire universe who was capable of activating the system. In that case, it's not an active backup procedure. The architecture can't tell whether it's weakly trying to connect to Animus or to Mary, it's just trying to connect to anything vaguely resembling the kind of entity that's supposed to be controlling it.