In WordPress 2.7, you will be able to update themes from in WordPress, as well as plugins. This is going to complicate those who have made modifications to the theme. Any modifications, currently, are going to be overwritten. That is to say that changes may be made in the future that will allow you to keep those changes. My point is only that if you are going to be modifying a theme, you should create a child theme instead and create the change there. All you need is the style.css with the Template: Parent-Theme-Name at the top in the CSS comment. You then can create files with the same name as the parent theme. Some custom files created for inclusion will not work this way, unless the parent theme specifically coded to work with child themes as well. Regardless, you can copy over from the parent theme and create the changes there. If you are only changes a file or two, then it will work out great.
You will be able to upgrade the parent theme, gain the fixes and changes there and still contain your changes. Eventually, the DIFF support will find its way into the upgrade process of themes, but I still think the heavy lifting would be better placed on child themes than depending on the diff support.