Yes, thats why Geany 1.25 has changed the notification to a bar at the top of the editor, it is only visible when you have the file visible and it is not modal so it can be ignored if you want to. But if you have the log file visible, I would have thought you would want to know there is more information available.
To be honest it's annoying before, I just endure it. In any case, there is always the button to re-read the contents of the file. And frequent notifications annoying once again.
The current modification time system is to alert users to things like someone else modifying a file you have open, or when checking out a version from VCS changes the file. That way you are more likely to make edits to the right version of the file.
Imagine that-be if each database when showing query result notified that visible data are not relevant.
First it would be very costly in terms of resources. Second on the tables with frequents inserts notifications will be blinks.
In general, I understand that I am not convincing. But the editing files is not a "chat" and not needed online here.