You could probably replace the version of rsync included in arRsync. It depends on whether or not they're bundling a copy of rsync with the application. If they are, I don't know why they wouldn't use the newer version. I'm guessing that they just launch rsync using the default OS version.
I have a command line script that I use to update files to various drives using rsync, but I'm using the newer version. I believe both SuperDuper and CCC both use this.
To see if the newer rsync is in SuperDuper it's usually inside the Resources folder of the application. You could check by doing the following:
1. Single click on the application icon.
2. When the icon is highlighted right click on it and when the menu comes down, click on show package contents.
3. A new finder window will appear with a folder named "Contents"
4. Double click on Contents
5. Another window will open. Double click on Resources.
If rsync is stored in there, you'll see it. You could copy (not move) it to another location and run rsync via the command line to see what version it is. If it's the newer version, you might want to try saving the old version of rsync to something like rsync.old and then moving the new one in its place.
There's no law saying a developer has to put that in Resources, they could put it anywhere if they like, they just typically do it in Resources. You could probably also try the same thing with arRsync, and possibly replace that version of rsync with the one from SuperDuper.
A lot of these are obviously kind of experimental, so be careful and make sure you save the originals somewhere safe before doing anything. rsync is open source so this shouldn't be a license problem of any type.