I use WinMerge to view changes to Subversion working copies. Every time I edit in my IDE the currently compared file I get a modal dialogue with the file was modified prompt.
As far as I know there's no way to disable that behaviour (the "Automatic rescan" setting just refers to changes made within WinMerge) and it'd be interesting to have the option.
Perhaps there could be an area within the window like:
File was modified externally (reload)
... and maybe a setting beside Editor/ Automatic rescan like:
☐ Automatic external changes reload