Most people only use Rename, Move, and Copy after files are already in their library in their final location. The new option was added because many of them have extra files such as subtitles, cover art, etc along with the files and they would not get moved when the main file did because they are not in the library. It is checked by default because many won't discover the issue until long after they have moved files and would require a lot of time to move them by hand. Worse they may not even be there any more.
So I think JRiver decision to have it checked by default is this: It may be inconvenient for you to uncheck the box, but for others it could be critical if they forgot to check it.