I don't know that we can answer "How" to any of the questions. We can at best speculate. I agree with you that not understanding how God has certain attributes, or how they work, doesn't prevent me from accepting that He has them as claimed. But my acceptance of those attributes as fact, doesn't mean I have to stop asking questions or speculating.
I thoroughly agree with your comment about asking questions and speculating. God gave us minds and He expects us to use them to His glory. He is glorified anytime we understand more of His revelation whether we uncover truth in His bible or in His nature.
The description (discovery) of gravity was not anti-Bible.
I continue to believe that the 3 omni's are separate because I interpret the bible to reveal them that way. I can think of no place where it indicates that one is dependent on the other. I can think of places where they appear to work in concert.