Hari Om & Pranaams!
From what I understand, the three gunas of Prakriti are perceivable in our day to day life. Since effect is inherent in the cause, it is inferred that Prakriti is endowed with these three gunas. The Rishis of yore did a lot of contemplation on this and came out with the theory of deliberate superimposition and negation to understand God.
In the end, there is only Brahman and nothing else. It is natural to assume a samashti for every vyasthi, otherwise the workings of Maya can never be explained. But we must always remember that it is all Maya and hence mithya. This logical theory is the one adopted in the shastras.
Ishwara is Brahman's instrument for manifestation. Hrnyagarbha, Virat and Isha, all exist within Ishwara. If there were no governing principle, there would be total chaos. On the other hand, we find that everything is in order. Order cannot happen by itself.
This is my understanding. I appreciate your bringing up this topic as the understanding of this topic will bring more depth to our knowledge.
In Shri Guru Smriti