By design, all custom metadata at the document level are propagated to all of its topics.
When updating a metadata value by web service, it was already possible to block the propagation of metadata values to all the topics of the document.
The control file for the most recent connectors (Word, FrameMaker, MadCap Flare, Markdown, DITA) has been improved to provide the same control on metadata propagation. For more information, read our guide to create a control file.