I'm using Confluence 6.15.2 but this does not seem to have been fixed as of 7.0.2: https://confluence.atlassian.com/doc/confluence-7-0-release-notes-973479448.html.

Adding new attachments to a page creates a new e-mail thread instead of using the e-mail thread generated with create content (POST /rest/api/content). When adding new attachments is done manually, it correctly concatenates to one thread.

This functionality seems to be on Confluence's side: https://confluence.atlassian.com/conf615/email-notifications-967338126.html.

"Email threading: Confluence will attempt to group all the email notifications about changes to a specific page together."