JarodRussell wrote:
Math describes the patterns in the universe.

Yes, "describes" the patterns because math is a language with formalized structure to make it a precision tool. But math is not the patterns of the universe itself. That is what I meant when I said that math is not "truth."
That was also the intent of my Ptolemy and Kepler analogy—they both used math to model the universe. Both believed the universe to be mathematically perfect, and Kepler had the courage to question his own convictions when data from Tycho was stubbornly uncooperative. How could either of them be wrong if math was used to get the answer?
We may be missing each other due to imperfections in another language. The following article is food for thought. (Please note that the author is an electrical engineer, not a "theoretical" physicist):
The Reasonable Ineffectiveness of Mathematics
By DEREK ABBOTT (PDF)
So for any "being" inside that program, the programmed universe would work according to that weird logic. So if those beings were to describe how their universe worked, they would come up with a different math.

Ah, "they would come up with a different math," meaning math is a language and not some Pythagorean "truth" embedded in the "fabric of the universe," to use a Greeneism.
The above statement suggests that you believe the universe is "intelligently designed" software, or maybe a hologram. Perhaps it is. But "we don't know" is a more accurate answer.
One of my gripes with many mainstream theories is the presentation of conjecture as fact. Such as, the universe had a beginning, exploding out of nothingness and creating space itself. Or the notion of superposed states of being—also known as alternate universes—derived from quantum mechanics. In the latter example, there is no way to test such an idea. Schrödinger's cat was intended as a parody of the multiverse idea, yet many actually use the analogy to teach the concepts of QM. "The cat is both alive and dead at the same time, until someone opens the box thus sending a particle backward in time to establish the observed state of the cat."