My use case is this. I like leaving empty lines in between my code sometimes. I also like leaving indents on those empty lines so that when I go back to them, I don't have to manually indent every time.
I only want to show whitespace highlighting when at the end of a line with other visible characters on it, and only if my cursor is not at the end of that line.
I didn't see a config option for that in your documentation, so perhaps you can take this as a feature request.