Currently, we only have the option to reply to a specific thread, which means it adds the reply as the last email in that thread. However, in reality, we know that people might want to reply to an email two ago because the thread itself has been merged with multiple conversations. Spanning a few departments

In the UI, you can simply reply to that specific email, but it's not possible via the API, which means it's not possible for AI agents.

Maybe this will be also covered in your planned MCP update, but is not available currently even in your API.