I think it is basic that ally vessels ping each other constantly so should have no problem identifing ELS copies?
It is about the extreme lucky, optimistic outcome of world
We probably won't have Aeolia who discover GN particle and use it on selfless plan betting on humanity's chance between a dictative Ruler Ribbons and Innovator Setsuna.
They are lucky Setsuna survived both seasons and successfully reached the outcome Aeolia wanted, and they are lucky again their dialog with the first outer species is a relatively sane species who willing to communicate if you know the way.
Hence happy ended.
All of above is just an extreme happy ending, but the sad thing is, Theta still trying so hard to reject it entirely, CB is NOT aimed to fight gov, Aeolia just wants to have a genuine Innovator and a 00 so people can realize the value of understand each other, and he knows humanity have no time when he found out the coming dialogue is near.
But for me, alien such like ELS if they are coming at us, this level of threat is way way out of our capable by using conventional way to deal even with given hundreds more years to prepare, human will lose even having thousands of Aeolia flag ship's large particle laser.
Well imagine us as the Earth island in a global international situation, even Theta would agree with at least we need to act like good right because it is practical for a so weak and young civilization like us, isn't it? So that we might get help from relatively lawful superpower or at least will not become pawn of barbaric superpower being used and then tossed away. Then what else the reason Theta rejecting 00's message?
But well, I know the opinion from Theta is honest from him, so lets leave this matter to future Aeolia in our world lol.
BTW to me, Armored Core 6 have similar conflict too, they discovered a type of plasma fluid-like particles capable to inhabit data and consiousness called Coral + real level of human nature ugliness endless conflict, therefore most of their ending is just suffer and not ideal, I think Theta might like AC6 world then, I enjoy both but especially AC6 it is so real and well written.
Conclusion, if we human can be released from the cage of body, we can communicate only with true intention, so that all conflict will become productive, the source of twist is always being able to lie and hide.