I'm assuming you mean there are non-algorithmic uses involved, since specific build orders are easy to program. I can't actually think of anything crazy here.
No, it has to do with how the AI's production bonuses work. A free early Settler or Worker means a lot to me; it doesn't mean a lot to the AI, because it can spit them out like mad anyway. Ditto a universal +2 Food (AI's tiny food boxes), a free Wonder (AI's tiny production boxes), and a sizable early Culture buff (AI's tiny production boxes and unlimited gold -> Culture building spam). Finally, the Culture buff means you can easily reverse the city tile
nerf with Republic. Acquiring most of those bonuses before the first expansion wave, and the remainder during the expansion wave due to the new Legalism is very possible. It's also desirable to do so, since many of those SPs are more desirable than anything other than Freedom.
As you noted, speeding up Babylon's ability to rip through the tech tree with a free GS isn't a great idea either. That and +1 Scientist/University is why I consider Babylon to be a candidate for the strongest post-patch civ. France is a candidate due to the faster SPs, although the potential for early Culture bonuses for all civs mitigates that somewhat. Free food and mad growth bonuses clearly strengthen India, and Siam will still have a strong early game due to increased Food/Culture and the ability to bypass Libraries. It's worth noting that all of those civs also have worthy UUs.
Persia is also substantially strengthened on Deity, since it will be possible to get Chichen Itza with the Meritocracy GE. I don't think that's sufficient to make them the best civ, but it's not out of the realm of possibility.
Let's not forget multiplayer. Since the best strategy is still to grab honour and chop rush the best early unique unit and go smash someone, you need to elevate other policies to compete.
While this is true, until they fix multiplayer's plethora of problems this seems a secondary concern. Even then I'm not sure it matters, since the only possible defense against a rush will still be a rush.