I think the refugee parallel is clearly intentional. Personally, I find it heavy handed, one-sided, and not at all artistic in nature. It's a good/evil declaration. A way of making a modern day statement.
I would also point out that there's a letter in the Baldur's Mouth basement talking about making sure pictures of Gortash don't make him look too orange. Like a pumpkin. Doesn't take a lot of literary analysis to figure out who the tyrant in the game is representing.
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A story can be told without being this heavy handed. With letting the themes within the story grow organically and speak for themselves. So, I don't accept the "all stories are political" base line response.
But I also don't expect anything else. We've gone through years of this. It's not possible to drink a beer or play a game without someone dragging in their politics. Would that we lived in a different world, but alas, we do not.
I agree that the game is heavy-handed with real-world parallels, but I don't think it is wrong for a game to draw from contemporary issues as inspiration. The problem here is the obvious heavy-handedness, as opposed to being "political." Subtlety is an art in itself, and while Larian has mastered many arts, this one isn't it.
However, I would like to say no one is forced to play games with different political values than their own, or with values they don't like. There are plenty of games out there, and if something is a dealbreaker, it is advisable to go play a different game, rather than put down artists for incorporating their own views into their work. While games are mass-consumed products, they are also art pieces, complete with an expression of self. Now, that self may be 400 selves, but it's still a perspective of its own, with a legitimacy to its views in its own way.