Thank you for your question!
Dear soul, I understand your confusion.

Here is a little background information. This Gyan is explained under the influence of devotional Hinduism. That is why, you have 3 names of “beings” who have a repercussion in Hinduism. You have Brahma known as the “creator,” you have Vishnu known as another incarnation of God and then you have Shiva (in the Hindu trimurti) which Brahma Baba changed to “Shankar” (even though both names refer to the same “deity”) so the difference between God Shiva of being above anyone else could be made.

You know what is the easiest solution?
Forget about all of that. It is not necessary.

Here is the simple explanation without any religious background.
God is the Supreme soul.
The forces of the Drama, which is perceived as “creation,” sustenance” and “destruction,” has been assigned in devotion as the “3 acts of God.” Those 3 acts, have been given names such as “Brahma,” “Vishnu,” and “Shankar.”

Because Brahma Baba is the “father of the Brahmin clan,” and known as “Prajapita Brahma;” Brahma Baba has taken the “spot” of “Brahma” in the trimurti of Hinduism.
That “creation” grows. That is known as “sustenance” and it is represented as “Vishnu” in devotion. That sustenance decreases in “celestial degrees” through time and disappears for “1 second.” That is “Shankar.” Then, Brahma emerges again to continue on in this everlasting cycle.
See?

In a more scientific way we can describe the same thing as; “matter cannot be created neither destroyed. It only transforms.” (First law of conservation of matter and energy.)
What exists (creation) gets transformed gradually (sustenance) until what it was there before, is no longer visible (destruction) for it has converted itself into “something else” (creation.) This cycle lasts 5000 years before the “original” point of reference repeats again.
See?

Or we can say the same thing as when we say that “Brahma emerged from the navel of Vishnu.” Destruction (Shankar) being the “1 second” of separation between the form of Brahma and the form of Vishnu.

As you mentioned, “Vishnu” is a representation of the “perfect couple,” or Laxmi and Narayan or the Golden age or Brahma is his highest stage, etc. Shankar is just the “1 second” destruction that occurs for “one form to change into another.”
See?

In the Sakar Murli Baba uses “Vishnu” and “Shankar” as if they were living beings in the subtle region. That is not so. That is just devotional understanding which needed to be added so the important concept of “trimurti” and “karankaravanhar” (God acting through others) could be digested with the “new knowledge.”

This is why, many times I have mentioned that “pure” gyan does not require Hinduism to be properly understood. As you can see, to fit gyan into a “Hindu” background, brings its challenges and may add confusion in some aspects of gyan.

Hope this clarifies your question. 🙂

Best wishes!