I can only imagine "universe" is supposed to be "Earth," so I'll proceed with that in mind.
If I was an atheist, I would not have the advantages of rational thought gained since the Enlightenment, but there were atheists and skeptics at that time, to be sure. I might have thought the Earth was flat, sure... but you imply that I would be wrong and that an underlying truth of a nearly spherical Earth would be waiting for me while I was sure the Earth was flat. That is, my "science" would be incorrect while "God" would be waiting in all his Mighty Correctness. In this case, the truth would not be what it first appeared to be, you're right about that... but your example quickly becomes useless.
A ruse easily seen through, and not well thought out. Your example is carefully set in an age when rational thought was not what it is now, but even so, it is science that first discovers that the Earth is not flat... and religion that kills people for saying so, since "God" said it was flat. And contemporary science requires a wealth of evidence and peer review, so scientific theories are not wild guesses, as might have been case in 400 A.D.
The "flat Earth" was the interpretation of the day -- but make no mistake, it was a religious interpretation. As facts began to stack up against the theory, early thinkers began to wonder if, in fact, the Earth was not flat. In other words, science changes as evidence appears whereas religion only changes when science has embarrassed it into doing so... unfortunately, after many have lives have been lost, in some cases.
Your implication of a truth different that what is now known is a situation that has already played out over and over... and science has shown over and over again to be accurate where the Bible is vague or completely useless. And the Bible is interpreted a new way every minute. Try counting the number of Christian sects in the world today. I dare ya.