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That's in the Preamble of a document that has no legal force. As you know. Roughly half of the Founders were not theists. They did not believe in a creator god. I believe they only used that phrase to convey the idea that the rights were independent of any human decrees, as you said.
But yours or my opinion about a right is irrelevant to whether it exists in any given society. I find slavery heinous. That doesn't mean it is somehow sacrosanct. Theists actually ask that question as a "gotcha"..."where do you get your morals, where do you get your rights". It isn't a deity. It's my opinion, argued (much better than I) by smart folks for centuries, that then became a part of the societal culture and norms. Slavery is bad because we think it's bad, and for no other reason. At various points in the past, society was either conflicted about that, or actually supported it. Today, we don't. Morality and rights are -in a democracy- a consensus of opinion, and what is written in the law (including the Constitution). All of which is subject to change/revision through whatever processes are described in the laws.
Which is why I have hard time looking back as Jefferson and saying "he's bad because he had slaves". For that time period, he was conforming to societal norms. Today, he would be a pariah if he engaged in that activity. Most (or all?) of our Founders would be castigated when viewed through a 21st century lens.