compare-windows-whitespace is a variable defined in `compare-w.el'.
Its value is

Regexp or function that defines whitespace sequences for `compare-windows'.
That command optionally ignores changes in whitespace.

The value of `compare-windows-whitespace' is normally a regexp, but it
can also be a function. The function's job is to categorize any
whitespace around (including before) point; it should also advance
past any whitespace. The function is called in each window, with
point at the current scanning point. It gets one argument, the point
where M-x compare-windows was originally called; it should not look at
any text before that point.

If the function returns the same value for both windows, then the
whitespace is considered to match, and is skipped.

You can customize this variable.

This variable was introduced, or its default value was changed, in version 24.4 of Emacs.