The short answer: it doesn't matter.

The long answer is the universe (or multiverse, or universe of multiverses, or whatever) is clearly a system that works because here we are despite the spectacular (and not-so-spectacular) ways it could fail at so many levels.

If it's a system that works and we're in it, we're never going to be able to model it completely or perceive outside of it, because that would entail just a bigger system that we're also in. Moreover, there will always be a gap between the actual universe and any model we can construct of it; there will always be a source of new phenomena to observe, so we shouldn't worry our pretty little heads about it.

But if there is, say, an entity that can appear to intervene on physics in ways that are interesting to human beings, it is necessary that it be part of the same system we are, which is to say equivalent to a very technologically-advanced alien. It is important, of course, to recognize that that is not the same thing as a deity. I'm sure there are plenty of entities out there that might superficially qualify, but we have yet to produce a viable specimen.

Now, if there was an entity that was truly capable of intervening on the fundamental elements of our system, it would necessitate that it was on the outside, which would mean that all information moving across the system's boundary would be constrained to manipulating the rules of the system itself. But in that event, how could anything within the system, that is how could we, perceive the difference between an intervention and any other natural phenomenon?

Of course, if I'm wrong, then Gödel is wrong, which compromises mathematics, which compromises science, which compromises technology, which basically makes us all subject to the caprice of some big sadist in the sky. And that isn't a very fun existence in my opinion.

Therefore: it doesn't matter.