It seems likely to me that the 6-episode version of Good Omens season 3 always went roughly this way, and the script was cut down to 90 minutes instead of being rewritten into a clear, satisfying, 90-minute arc.
With that thought in mind, it makes me wonder what the missing pieces would have been, and how they would have built up to this ending feeling like a clear fit. I.e., how do we get from S1's Adam being convinced not to replace his friends' parents and S2's Sitis saving her children to S3's clean slate approach?
I think there are snippits within the remaining 90 minutes that hint at how the necessity for rewriting the universe could have been supported by what was in S3.
The decay of Whickber Street could have been a case study in it: Aziraphale left, and in the span of just a few years, it utterly collapsed. Why? Well, Aziraphale wasn't there supporting it. When he lived there, he wasn't just passively failing to collect rent; he was supernaturally molding the environment around him to provide sturdy buildings that don't require maintenance, protect it from gangsters and government inspectors, and everything else to ensure that he and his neighbors never encountered any serious problems.
Tadfield could have been another case study: We saw at the end of S1 that Adam kept his powers. The first newspaper headline in S2 says "Is Tadfield the Best Village in England?" Adam presumably kept using his powers to make it a wonderful place to live, with idyllic weather, no devastating highway construction or predatory corporations moving in, and neighbors who never moved away. Adam renounced being Satan's son, but even without his conscious meddling, he still kept Tadfield intact.
Crowley's plants are a case study as well: Without miracles, he has only one left alive, and it doesn't look like it will last much longer.
Aziraphale leaves, and Whickber Street crumbles. Adam stays, and Tadfield remains. Crowley loses his miracles, and his plants die.
Why can't the current universe exist without God? The same reason Whickber Street can't exist without Aziraphale.
To lean into the trend of angels and demons pairing off (from S1's Aziraphale/Crowley, S2's Gabriel/Beelzebub, and S3's Muriel/Eric), this could even be because of angels and demons, not God Herself.
We only ever see Aziraphale and Crowley stationed permanently on Earth, but in S2, Shax calls herself "Hell's representative in London." The implication is that there are hundreds or thousands of angels and demons stationed all over the world.
Perhaps they're all constantly, subconsciously keeping things running, the same way Aziraphale does with Whickber Street, Adam does with Tadfield, and Crowley does with his plants. They don't need to be purposefully trying to keep the world running; their desire to have their own small part of the world be nice is what keeps the whole world worth living in. (And isn't that a nice thought, by itself?)
Telling them not to meddle wouldn't be good enough; they're meddling subconsciously, all the time. The bookshop has no rats because Aziraphale is an angel. Shutting off their miracles wouldn't save the world; it would crumble, just like Crowley's plants.
The existence of angels and demons was built into the fabric of the universe, and they can't be removed from the ecosystem without everything falling apart. The only way to have a universe without supernatural meddling is to change the very fabric from which the universe was made.
I'm not saying this is the ending I would have written myself. Looking at the pieces that still remain in S3, however, this is my current best guess for how they could have built up to this ultimate conclusion.
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