"Have the faithless not regarded that the heavens and the earth were interwoven and We unravelled them, and We made every living thing out of water? Will they not then have faith?" - Qur'an 21:30
"Yara" is also used to refer to understanding or thinking something ("seeing" in the mind).
It may also be used here because this is a mental observation or understanding that can be deduced from what is seen. Firstly, one can see the existing universe and deduce that this could have happened. Second, one can engage in scientific observation of the universe and deduce that (to our knowledge currently) it is expanding and was once essentially "closed", or that living things on earth are water-based, or that life may indeed have emerged from water.
That is, we "see" the original state of the universe and earth mentally through "seeing" the current state of the universe through observation. So in that regard, both types of "see" could be meant (the physical seeing now, and the mental seeing to use scientific deduction).