I've been doing a bit of digging on this issue, and I've discovered that cartoons that depict real places are basically never prosecuted, while most movies (with real footage) can be and have been prosecuted.
What this suggests -- from a laymen's perspective -- is that level of detail is important. If you just make some vague depiction of the interior that really looks very little like the actual, then you're in the clear. If it's a literal moving film of the inside, then you can get in trouble. What about something in between, like Resistance? It's not literally a real depiction, but it's precise, accurate, and deliberately as close to the real as possible. I'm not sure if that's legal or not, but it doesn't sound like the church is making an absurd claim here. They may lose, but it doesn't look like they should get laughed out of court or anything. This is right on the cusp of legality.
Again, disclaimer: this is just 30 minutes of research and logic. I'm not an expert.
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