@theducks - it is a limitation of metadata download plugins. A gui plugin like Count Pages or Goodreads Sync has no such limitation.
Metadata download plugins do not have responsibility themselves for saving data to the database. Instead they just return some data in a structure that calibre code then merges across metadata plugins and then saves. So no matter what a metadata plugin does in terms of "attempting" to pass back custom column data, the core calibre code just ignores it because it knows nothing about it.