The religious systems in Civ6 is uncontroversial because it's extremely christian-centric in its game mechanics, with apostles and missionaries at the core of the religious gameplay. They added gurus and you can choose traits that aren't based on christianity, but overall it's based on the way christianity worked, with apostles defining the initial doctrines, and missionaries expanding the faith. It kinda works for buddhism too, but that's all.
Even for the other monotheistic faiths it just doesn't work, as historically judaism is an ethno-religion and islam didn't use missionaries or apostles, but instead military force, then trade, as well as specific laws that favor muslims.
If Civ6 had been developed in another part of the world, its religious system would be completely different.
But really it's always like this in Civ. the game design is imbued in traditional american values, like the belief in progress, capitalism, the benefits of war, essentialism, and with civ6, even the way women and native people are represented.
It's not controversial because people from other cultures see it clearly as an american product.