It's more a debate between people like me, who see the narrator of the songs as being a faithful/religious person struggling with or just affirming their faith, and those that would argue that every mention of God is somehow metaphorical, which makes very little sense in almost all of the songs. The basis for the God as metaphor is due to Trent's subversive early 90s image, despite the fact that he's recently affirmed his belief in God without subscribing to a particular religion.
So, yeah, we know. But there's a debate over what he means by "God." I don't see any of the recent mentions of God being at all antagonistic, mocking or confrontational, and I don't get how or why an atheist would bother talking about something they don't think is real that often, but some think Trent is a Marilyn Manson level anti-spiritualist based on the bitterness expressed in songs from the late 80s or early 90s. Shrug.