Im left to assume that while the stones were out of their hands it was enough to open the gate but I think the issue here is that they dont have a very good internal communication network in their organization. Mathias is a great example where you see that Lyblac has gone around manipulating all these people but once they serve her purpose she moves on. Had she tried to coordinate these efforts and not compartmentalized them she might have succeeded.
There's a lot of examples of the left hand not knowing what the right hand is doing. And this is mirrored by the audiences lack of knowledge as well. We were all in the dark.
I think Mithias's plan would be less of a threat because you would have a man infused with Galdara opposed to Galdara reborn.
Would like to put over just how unique this method of story telling was. I have never played a game that felt like a mystery so much as this. 80 hours and I didnt realize there was mystery at all and then suddenly there is this "ah ha" moment that I have never got from any game off the top of my head. At first i considered it a criticism that the story was section off the way it was but in hindsight that allowed for something truly unique.