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The release notes for the latest version of After Effects states that MKV files are supported, but neither 18.4 nor the latest Beta can import them.
They aren't included in the 'supported file types' in the import dialog, and if forced to import by setting the file types to '*.*' random errors about file types are thrown up, depending on which codecs are embedded:
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Good catch. This feature was supposed to go into beta but has been delayed. Stay tuned for updates.