Focusing on "endowed by their Creator" as a statement of theology is incorrect.
It was a statement of political philosophy; it is simply a rebuttal and rebuke to the British Monarch's "divine" right to arbitrarily rule, nothing more.
Read some of the works the framers used to frame this republic (Locke, Sidney) that outlined this new concept of inherent rights and the concept of "legitimate" government. Each and every one was written as an indictment of the Crown and as rebuttals to other political treatises (Bodin, Filmer etc) endorsing the monarchy and validating the King's "God given" power (from direct heredity from Adam).
The statement that our rights are "endowed by their Creator" is only establishing a maxim guiding the fight for independence, that our rights are not gift from the magistrate but are an innate part of us that we bring with us before we enter into a social compact (government) established to protect those pre-existing rights . . .
"We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.--That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed, . . . "