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A metadata instance will contain custom field information only if someone has put it there. Because of that, I think you are facing at least two problems.
1) If you are creating a Metadata instance yourself, then it will have no knowledge of custom fields. The only way I know to get a complete Metadata instance for a given db/custom column set is to use library.database2.get_metadata.
2) Assigning a metadata field in the mi structure has no effect on anything. Something later must take that data and put it into the database. I have no idea where that happens, or how it happens. That said, it is highly unlikely to work unless the code calls the set_metadata method in database2.
My guess is that the plugin doesn't know about the database (doesn't have an instance of an open db), in which case you will not be able to see custom field information. I am uninterested in plugins, so I can't give you any more information than that.
FWIW: the 'other' argument to the constructor is expected to be a Metadata instance, not some random dict.
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