After several years I came up with a logical explanation of how Dark started, and I want to share.
H.G. Tannhaus machine didn't create two alternate universe but rather alternative universes with different levels of similarity already existed.
In the "origin" world 1 Tannhaus actually ended up building a machine which opens portal to alternative dimension. Which makes this event the origin of the knot.
Instead of traveling back in time Tannhaus ended up traveling into another world (2) in which nuclear plant was greenlight for building and local Tannhaus 2 built the time machine and a time portal. So this world ends up with time traveling and dimension traveling tech.
In this world all kind of time traveling incest happens creating a mess resulting with Jonas and Martha having a child, the Unknown. As Jonas grows up into Adam he wants to destroy this loop, Eve wants to preserve it. War happens in which Adam 2 destroys himself from existence entirely, including young Jones thinking this will end the loop entirely, because Adam doesn't know the true source of the knot is in the origin world.
Eve has the tech to travel through time and dimensions, so before Adam 2 deletes himself she sends her agents and young/mid/old Unknown into world 3.
In world 3 Tannhaus originally didn't manage to invent a successful machine. None of these loops had happened yet.
But Eve's group time/dimension travels and manipulates events in world 3 to recreate it in the image of world 2. Ensuring Jonas 3 will be born, so Martha 2 can conceive Unknown with him.
With Unknown traveling as his young/mid/old all at once bulleproof paradox is created. His existence and everything he does is set in stone. The only way to untie the knot is to prevent the origin of the knot.
So even when Adam 3 tries to destroy pregnant Martha 2 from existence, nothing happens.
Claudia 3 ends up killing Claudia 2, assumes her identity, travels to world 2, infiltrates Eve group and finds out about the events in world 1 which started this whole mess.