The JMS tool is used to create the DB tables used by the extension and not to execute the specific code that would be present in the installer of the extension and executed to perform the migration or upgrade of the DB layout.

JMS does not change the DB layout the table used by the extensions once they are created.
When you upgrade or migrate an extension in the master that impact the DB layout in the master, this does NOT update the DB layout used in all the slave sites.

To allow the extension re-apply their specific stuff to modify the DB layout, you need to re-install them in the slave site to let the extension perform their specific DB modifications.