After looking at (Q)Scintilla for some time now it starts looking that implementing WinMerge-kind of file compare is not possible. The editor (rightfully) assumes that lines in files are sequential. But WinMerge GUI would require adding some missing lines between lines to synchronize files. That kind of GUI might not be possible to implement without modifying editor components themselves. And that is something I'm not interesting in doing - after having lots of problems in WinMerge with it. Implementing properly might take same time than most of the other porting work.
So what are alternatives?
I think the only real alternative is to implement "mapping" area between editor panes. Like many other compare programs do.
I'm keeping wiki up to date when I'll progress. I've written about this problem to: http://bitbucket.org/kimmov/winmergeqt/wiki/FileCompare