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I'm not familiar with Natron, but have you used the Crytomatte plugin to extract the mask information? Otherwise, could you attach the .exr so I can test it out in Nuke?
Works fine in Nuke when using the Cryptomatte plugin to Extract the Mattes, it is jagged if you just shuffle out the Cryptomatte channel (there is additional data in the other cryptomatte channels that is required). It seems available for Natron as well. Try it out.
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