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I'm most confused by the overworld models being to scale and most battle models being to scale, but seeing that apparently Mewtwo is an exception. Even Onyx seems to maintain the correct scale throughout, so I wonder about that, if there are any other exceptions and, if so, why they exist when the maximum and minimum range is so manageable in this situation.
Maybe the scaling is engine inherent/automatic and the relative z-axis proportion due to its tail lenfth and orientation somehow calls for Mewtwo being adjusted?