PHPBB has no settings that control this. Either you get notified about every new reply, every time, or you turn it off.
Sorry, normis, this is patently false. This worked fine in the past. If you take the time to read the text of the email message, it even says so:
You are receiving this notification because you are watching the topic
"v6.42.1 [current]" at "MikroTik". This topic has received a reply by
strods since your last visit. No more notifications will be sent until you
visit the topic.
This behavior changed in January. Stuff is now broken.