This is entirely why the scientific method doesn't work when proving for God.
If you believe what you say, here, then you must simultaneously concede that your "proof" (i.e. the link you keep pasting over and over) is not proof at all. Either you believe physical evidence can prove God's existence or you don't. You can't have it both ways (and, furthermore, there is a correct answer despite your beliefs).
So, which is it? Do you believe it is possible for physical evidence to prove God's existence, or not?
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The universe includes everything. But, because of Who God is, the universe might not include God. Or God might be both within and without the universe. Or God might fill the universe as well as being within and without.
I find it easier to just stick with defined sets such as "real" and "unreal." Using the phrase "Universe" isn't necessarily bad, but it does us little good to reference if there are instead multiple or parallel Universes that we cannot observe.
By sticking to "real" and "unreal," it doesn't make any difference how many Universes there are. It also helps us avoid potential problems that you're alluding to, here. If God is real, he is included within the set of Reality, and it doesn't matter whether or not he exists in this Universe.
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There is no other meaning for "the universe" than "everything." So, science can't work with God the same as it works with the universe.
Again, this problem is avoided by sticking to the sets 'Real' and 'Unreal.'