By using the Settings window of this plugin I set the color of a Changed Line to some dark green color. In that way it works fine in both Light and Dark mode of Notepad++

In "Dark mode" Notepad++ uses white text, so when using light color the text is not readable anymore.

It would be nice when this Compare plugin could get a seperate set of colors to use in Dark Mode. And with the default colors a user should still be able to read the text.