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Let's consider a computerized virtual reality universe inhabited by digital beings that have achieved intelligence comparable to ours.

Mine or yours? ;-P

When they try to extrapolate what might have occurred before that beginning, perhaps they also come up with something similar to a multiverse concept. It seems to me that these digital beings would be completely justified in considering the possibility of an intelligent creator of their universe, particularly since in their case, that would be the correct assumption.

Having a justified opinion is not the same as it being correct. One can have a justified opinion based on current evidence but which is later proved to be incorrect. One can also have an unjustified opinion which is later proved to be correct. The outcome (or reality) does not mean that their opinion is justified.

Consider a lottery. If someone picks numbers based on someone's birthday because they think it's luck and those numbers eventually come up, were they justified in their reasoning? No. They were lucky.

Technically, I agree with you. They would be completely justified in considering the possibility of an intelligent creator of their universe but without evidence that would not be a justified belief. I have considered the possibility of an intelligent creator but the more parsimonous explanation seems to be that there is a natural cause. That doesn't rule out the possibility of an intelligent creator. There simply isn't any evidence to justify the additional factors, particularly when one suggests a specific god.

Why is the consideration of an intelligent origin of our universe now an inappropriate appeal to the supernatural?

An intelligent origin is by definition supernatural. It is outside of nature. That doesn't mean it's wrong but we can explain nature. Why should we consider something supernatural without evidence?

Not sure why assuming the origin of the universe is simple is consistent with science, but assuming a complex origin is not.

Because the scientific method excludes unnecessary complexities. If a simple explanation will suffice, there is no need to add flourishes to it. As regards the origin of the universe, we don't yet have an answer but it's more appropriate to adopt the simple explanations (even if they are difficult) than to adopt the complex explanations (even if they are easy).

It's easy to accept that a god did it and it's hard to grasp the complexities of fundamental physics but that doesn't make a god a more simple explanation because the origin of a god would need to be explained and the creation of the laws of physics would also need to be explained. That's why phrases like "the Lord works in mysterious ways" were invented. It shuts of lines of questioning. The natural explanation is simpler than one with a natural and a supernatural element.

Until it can be shown that the more complex explanation can describe the situation and the more simple one cannot, the more simple one is preferable. The problem is that any explanation with a supernatural element cannot ever be proven right because we cannot test the supernatural.

Therefore, the natural explanation might be proven right but the supernatural explanation cannot (barring whichever god demonstrating their power unambiguously).
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