Interesting, thanks for the investigastion. From my experience it feels like something with getting the focus back to the file. as if “Ctrl+R” is leading to have the focus on the current file lost, after the reload it is regained. When the focus is regained, the check for modification kicks in and if the file was modified in the mean time, it asks if the file should be reloaded. If the focus is lost, maybe it is possible to reload with Ctrl+R without having the focus lost?
Reading your posting reminded me on the first posting in this thread and the sidenote: since “Monitoring tail -f” doesn’t work as I expect it.
The “eye-button” also known as since “Monitoring tail -f” would solve this issue, if it worked as I’d expect it. I experience the same as here: https://github.com/notepad-plus-plus/notepad-plus-plus/issues/4955