This is only the case in a world-view that accepts that Omega cannot be tricked. How do you know Omega cannot be tricked?

By hypothesis, this is how it works. Omega can predict your choice with >0.5 accuracy (strictly more than half the time). Regardless of Free Will or Word of God or trickery or Magic.

The whole point of the thought experiment is to analyze a choice under some circumstances where the choice causes the outcomes to have been laid out differently.

If you fight the hypothesis by asserting that some other worldviews grant players Magical Powers From The Beyond to deceive Omega (who is just a mental tool for the thought experiment), then I can freely assert that Omega has Magical Powers From The Outer Further Away Beyond that can neutralize those lesser powers or predict them altogether. Or maybe Omega just has a time machine. Or maybe Omega just fucking can, don't fight the premises damnit!

And as wedrifid pointed out, this is not even the main reason why the smarter two-boxers two-box. It's certainly one of the common reasons why the less-smart ones do though, in my experience. (Since they never read the Sequences, aren't scientists, and never learned to not fight the premises! Ahem.)