It is quite possible that universes can exist without presiding deities. But it should be noted that there is no universe without Parabrahman.
Any universe undergoes three states: creation, preservation and dissolution. Technically, universe is a result of creation. Universe does not exist during dissolution. It is apt to use the word creation rather than universe.
Each creation may have different conditions in almost all aspects. All creations may not be same like the universe we are living in. The only entity that remains same in all universes is Parabrahman. All the remaining aspects can vary.
In the same scripture Yoga Vasishta, Bhusunda enumerates various types of creations he remembered. He saw large number of creations and told to Vasishta about some creations among them, which he remember. They are covered in two sections: section 21 and section 22 of Nirvana prakarana.
Some verses that are related to the question are as follows.
I remember the creation of one sole body named Virat in this world,
when it was entirely devoid of men and asuras in it
I remember the sphere of heaven shrouded under a sheet of darkness,
and when there was no Indra nor king to rule in heaven or earth, which
had not yet its high and low and middle classes of men.
Some verses are saying about the entire creation and some other are saying about conditions at some particular intervals of times in existing creations. Likewise, the initial conditions, later positions and other aspects of all creations may be entirely different.