Atma is sometning that exist in the Creation

Atma is sometning that exist in the Creation, so is Prakriti. Atma has certain chracteristics, so does Prakriti. Both must therefore be created by the Creator, the ultimate single source from which everything can be traced back. So, if Atma and Prakriti are the creation of the same source, the Creator, they would by defintion have some affinity of ultimate source.

The chracters of Atma and Prakiti are also derived from the same source So, these two would have chracteristics that would draw them into some relationship of attraction and/ or repulsion or none interaction or inter-relation. If we observe that that they have interaction because atma is everywhere and even in a human body and so is prakriti. So, one can influence the other or be influenced by each other. The affinity is therefore is tge very design of the of their same ultimate source, the Creator.

If Creator is God and God is the ultimate source of everything including Atma and Pakriti, it is God who has designed the affinity of Atma and Prakriti. If Atma was not influenced by Prakriti, Atma would be nothing but the Creator, it source. Prakriti plays its dance as per the properties imparted to it by the Source, the ultimate God. Atma, according to the properties imparted to it by Creator, the God, can just witness Prakriti's dance. As a witness it may seem to get overwhelmed by the dance of prakriti, though in reality it remains totally unaffected. When Atma is totally unaffected by the dance of the prakriti, Atma assimed the exact property of God the Paramatma. Leberation from the ipact of the forces of Prakriti or Self Realisation occurs when the the individual realizes that he/ she is the Atma, unaffected by the Pakrit, the ego and desires vanishes and equanamity rules: the gross physical body is still subject to Prakriti but Atma rules makes the senses and the mind rest in equnimity without being affected by Prakriti's impact in the form of desires or eogo. Body does not act any longer due the influence of ego or mind. The illusion that Prakriti helps generate in the form od developing identity of ego and desires to drive the mind and senses, no longer operates.

That is liberation or Salvation that the Sadhaka had been concentrating on as the only desire. When Salvation occurs ven that desire also goes because that is the property of Atma or the Self.

why God has created such a complicated design, only God will tell you one day.

But it seems when Atma is always happy, Prakiti causes senses to feel both happinss and sorrow depending on whether desires are fulfilled or not.