In the notification alert flowchart here: https://docs.mattermost.com/_images/desktop_notification_chart.png my preference would be for the "Yes" branch of "Is the channel Muted" to go to a new decision box "Is Allow Direct Mention Notification on Muted Channels allowed in user settings?" the No output of the new choice would go to "Do not trigger", and the Yes output of the new choice would go to "Does the message contain other words that trigger mentions" decision box.
In the notification alert flowchart here: https://docs.mattermost.com/_images/desktop_notification_chart.png my preference would be for the "Yes" branch of "Is the channel Muted" to go to a new decision box "Is Allow Direct Mention Notification on Muted Channels allowed in user settings?" the No output of the new choice would go to "Do not trigger", and the Yes output of the new choice would go to "Does the message contain other words that trigger mentions" decision box.