Can I configure this tool to default the choice for each differing block to the left side rather than the right side?
Right now the workaround is to swap the sides, but this is slightly confusing.
Not sure I understand what you want to do, but perhaps the following will help. In the FileMerge.app UI, as soon as the file comparison window opens, you can press Cmd+A to select all the differences (arrows), then press the left arrow key to change them all to the Original file contents. You can then press the up arrow to return to the first change (ignore the NSBeep()). Then use the down arrow to cycle down through the diffs and if there's one where you want to change to the "new" content that's showing on the right side, press the right arrow.