I know you have planned to unlock the two panes.
However, it would be a very handy feature to be able to slide a small feature on the vertical slider to create an upper and lower view of the side-by-side files. The upper section can be scrolled separately from the lower.
This allows the user to view related differences in two different parts of the files. For example, when dealing with moved blocks that are more than a page apart from each other.