From the FMW Reader documentation (found here) it states that "the reader does not handle any information about custom (embedded or linked) transformers." and this might be the cause for what seems to be an bug, but is likely expected.
However, through testing this myself many of my custom transformers are also broken down into their parts with their custom_transformer_parent_name attribute values filled out. It seems that many of the custom transformers that are not broken down into their parts have what would be the parent name in the transformer_name attribute instead.
From this documentation (found here) it states that "for custom transformers, ,transformer_type] value can be either SubDocumentTransformer for Embedded Custom Transformers, or ExternalTransformer for Linked Custom Transformers."
Many of the features that do not have the custom_transformer_parent_name attribute values filled out and have not been broken down into their parts seem to be Embedded Custom Transformers (based on the above information) for me at least. I hope this helps!