I want this on a T-shirt

To assume that the universe is disorderly presumes knowing some esoteric objective truth about how the universe works. Since the field of natural sciences does not provide that truth (by design), and practices that do aim to provide that truth (metaphysics, religion, etc.) seem to have different versions of it, I would say that there’s a fair chance that the universe is not that disorderly and we just lack better models for describing it.

I don’t think God has any choice regarding math and logic.

The way I look at it, the absurd complexity that rule systems can get into is a check and punishment for the arrogant and the tyrannical. 'Look I designed these rules myself just follow them and everything will be fine.' Ah but what about this edge case. 'Hm, I guess we can add a few more rules.' Bam, next thing you know it's a Byzantine bureaucratic nightmare any your empire refuses to grow anymore.

Meanwhile, if you put honorable people in charge and trust them to do the right thing, they can figure things out ad hoc.

Unfortunately, mathematics suffers as a bystander. But the good news is that the muggles will always want to keep the eggheads around because they would rather die than think about the negative consequences of having their dreams come true exactly like they wanted.