In 12.3.3 we are adding the ability to define extra context menu items which are only shown when you right-click the files (icons/thumbnails on the left) in the Replace dialog.
The commands can use {filepath} to get the file which was right-clicked, and {filepathdest} to get the other file.
So, if you send a diff tool both files, you will normally want to right-click the top file to ensure they are sent in "source, dest" order.
Commands don't have to use both files, of course. For example, you could add a menu item that copies the right-clicked file to a special location before it is either skipped or overwritten. Such a command would only use {filepath}.