For modern version control systems, 3way merge support is a basic requirement, but many other open source diff viewers do not adequately handle 3way merges.
There are options that may pre-process compared files before Kdiff3 actually do a comparison - to ignore for example automatically generated dates and/or revision numbers added by commit hooks.
With selecting code in one window and hitting Ctrl+Y, then selecting some other code in second window and also hitting Ctrl+Y you can manually align the code.