For the double-underscore magic words __HIDDENCAT__, __NOINDEX__, and __INDEX__, Parsoid is missing the tracking category corresponding to this magic word. This seems to indicate that Parsoid is not actually invoking the legacy parser to handle these magic words, and so the resulting ParserOutput is likely to be omitting the proper index policy values as well.
The __NOGALLERY__ and __NOTOC__ magic words are handled in the same place of the legacy parser, and might also be missing some necessary behavior flags.