calibre does set the metadata manually after an upload, it's just that ever since the latest firmware update, the reader overwrites the metadata set by calibre with metadata read from the file. This only happens for books in the main memory.
If you care enough, you can try to figure out why it happens. metadata is stored on the device in the file media.xml in the main memory and cache.xml on the storage card.
Transfer a book using calibre. Dont disconnect the reader. See media.xml. Now disconnect. Let it rescan the collection. Reconnect and compare the new media.xml to the old one.
If you want to submit a patch for editing PDF metadata, you should submit one to the pypdf project (it's what calibre uses for PDF metadata handling)