With all the first parts of your post -- agreed. I would only note that whether one would call what governs the realm of angels "physics" or some other kind of stratum could be open to definition and discussion.
As to Nineveh: yes, it's a little tricky. Nevertheless, I don't think that one must conclude either that God lied or that He changed His mind. The first thing to remember is that, while it's correct that God never lies, it's His statements *as correctly interpreted in their cultural context* that are never lies. One can not acontextually grab a statement, take it to western extremes, and then insist there has been a contradiction.
So what's my point? Well, God did instigate the prophecy that "Yet forty days, and Nineveh shall be overthrown!" But there are different ways this can be interpreted. It can be taken as a scientifc-type statement, a completely precise, ineradicable, and factual proclomation. However, it can also be taken as a warning. To interpret it as a warning does not make it false; it just means it implies something slightly different -- that if things don't change, that will happen.
That is how it was actually interpreted by all who heard it. The people of Nineveh did not view it as clearly ineradicable, but rather, repented and pled for mercy, saying, "Who knows? God may turn and relent and turn from his fierce anger, so that we may not perish." And Jonah also knew, even before saying it, that it was not a certainty, saying, "O Lord, is not this what I said when I was yet in my country? That is why I made haste to flee to Tarshish; for I knew that you are a gracious God and merciful, slow to anger and abounding in steadfast love, and relenting from disaster."
So the people of the day did understand it as, at least plausibly, a warning-style statement and not a hard prediction.
My speculation was why God used this ambiguous type of speech and not something that was *clearly* a warning, like "Yet 40 days and Nineveh will be destroyed, unless it changes its ways." I think it was chosen precisely to be ambiguous and create complete panic so that there would be actual repentance, and not give the people the feeling that they definitely had God in control.
So did God change His mind? I don't think so. He's omniscient. It was always His intention to give them respite when they repented, though He would surely have destroyed them had they not.
So there's my take.