I believe it's simply a case of someone trying to create controversy out of good storytelling. If religion is important to a story at all, it's because the religion is a problem. If it's not a problem, it's not a factor. No one cares about religion in a story if it's not a cause of conflict. Would anyone want to sit through entire paragraphs of a fantasy novel dedicated to explaining the religious practices of the population if they weren't somehow directly involved in the overall narrative? Of course not. So why the hell would anyone want to sit through such information in a video game?
One of the most important aspects of telling a story is limiting the narrative to only factors that matter. To use an example, if you take the time to describe a sword on a wall, that sword needs to be there for a reason, otherwise describing it was useless and a waste of the reader's time. Maybe the sword is one given only to army officers of a certain rank, and thus helps establish who a character is. Maybe later in the story that same sword is used in a fight. But if you took the time to mention it, it has to be a factor. It has to have a point.
So unless a character's religious beliefs are a core aspect of their role in the story--perhaps they're a priest, or a shrine maiden, or a monk--it's simply not a factor. So when it comes to the overall religious practices of the population of a video game... unless those practices are a source of conflict, they are at most a very minor background aspect of the world's flavor. So any time religion is an actual factor in the game's narrative, of course it's going to be "problematized". If it wasn't, it wouldn't need to be talked about at all!