I agree that to see the Universe as a closed system, with God outside, is a poor way of conceiving things. It's also unbiblical, in that God is intimately involved with every aspect of it (his immanence): "in him we live, and move, and have our being".
Yet The Bible is also careful to distinguish God from what he has made "The heavens, even the highest heavens, cannot contain you."
So I can't go along with your reasoning, which seems to me excessively physical, that by the universe being open to God we must conclude that God is part of it (though he'd have to be all of it, surely). Arguments that speak about "God not being mighty enough to ..." are so subjective, as I said on another thread recently: they presuppose that we know what God wants to do and how, based on our human reasoning.
So your final paragraph can either be taken as sci-fi stuff, or as one plausible scenario. But in the end it's taking some of the few things we know from science and joining the dots imaginatively to make a theory of divine action, Incarnation, Resurrection and a bunch of other stuff we actually know nothing about. .
However, what I can wholeheartedly agree with is the simple statement: "God creates by choice, and controls all by choice" - because that's abundantly affirmed by revelation. It's interesting to push the boundaries a bit further to try and flesh that out, but in the end it's most of what we need to know about creation, and absolutely compatible with science (if you dispense with closed causal systems and the idea of "chance" as a cause of anything).