MAJOR SPOILERS AHEAD. TURN BACK NOW IF YOU DON'T WANT TO KNOW THINGS.
The Talos Principle (and for the moment I'm referring specifically to the main game, not the Road to Gehenna DLC), posits two fundamental qualities necessary for humanity: logic and independence. The former is the purely mechanical aspect of the game: solve the puzzles. Independence is the more interesting one.
If you follow the primary intended path through Talos, the message you will get is pretty obvious: Elohim was telling you not to be curious, not to explore or express yourself, but rather than accept his will on blind face you tested for yourself, and that makes you human. You didn't do what you were told; you were independent. But were you?
It's pretty obvious to anyone playing the game that ascending the tower is the "right" way to play. For those more dedicated players, they might choose the Messenger ending, but that too requires you to do disobey Elohim and ascend up to Level 5 of the Tower. So, though you are "choosing" to be independent, you're basically just doing what the game wants you to do.
The game is about choice, but the very nature of medium is such that choice is limited to whatever the designers allow. This is the fundamental ludonarrative dissonance that is inherent to pretty much any game that involves player choice, but is especially apparent here.
But hey, it's a good story, fun puzzles, you get what they're trying to say, so it doesn't really matter. Anyway, the real highlight of The Talos Principle is The Road to Gehenna, which is one of the few instances where not only did I actually play the DLC (which I rarely do) but I think I liked it better than the main game. I mean, I appreciate all the philosophy and worldbuilding in the main game, and it's an interesting concept, but the DLC is just more fun, narratively. And you actually do get a choice that matters.
Oh, also, an (I assume) unintended side effect of The Talos Principle using a Garden of Eden-style framing device is that it's basically saying that theists aren't human. Which is a bit of a hot take.