I do wish it elaborated a bit more on Yukari though since it seems to be implied that even in this final timeline she's actually aware of what Gaku did for her. And the bit about Gaku becoming unobservable yet Yukari still being able to sense her is something that felt like it should be elaborated on some.
i think it was subtlety explained. observing a system means the system must interact with the observer, so basically the observer is also being observed by the thing they are observing. because Gaku is observing Yukari, Yukari can observe Gaku in return. Yukari is still somewhat aware of what happened because she never got rid of her own quantum eyes. that, and im pretty sure God-Gaku is still inside that mech. final Gaku mentions how one of the robots seemed to be genuinely worried about her when they were rescuing her from the serial killer. that one is God-Gaku.
Also I might be overlooking something but it does seem like there's a fairly obvious plothole with the phone: If Gaku talking to herself is merely symbolic and she actually gets the memories and knowledge and such from her alternate selves as soon as they start talking then surely that call should have given her a ton of knowledge about the situation?
it depends on the Gaku that she contacts. she doesnt get the knowledge of every Gaku, but only of the one she is talking to and any knowledge that Gaku may have gained. she could be calling someone for the first time, it could be their tenth time talking to someone. obviously, the further that a Gaku gets into her quest, the more knowledge she passes, but theres also the risk of super-knowledgeable Gakus dying (taking their info with them). basically, you gotta remember that all the Gakus talk to each other one at a time and they arent guaranteed to talk with a Gaku that has more knowledge than they do. like they say, they aren't light. they cant take every path at the same time.