Yes, it would be wise to compile your own copy of rsync, not only because the version included with any GUI program may not preserve all metadata, but because even the copy included with OS X itself doesn't preserve all metadata(!).
I'm on Lion, and here is is what the output from the system rsync reveals:
protocol version 29
64-bit system inums
64-bit internal inums
Now, here is the default rsync I use, which was installed via MacPorts:
protocol version 30
64-bit long ints
As you can see, not only is the bundled version out of date, but it hasn't had the required patches applied to insure metadata preservation. It's the same in Mountain Lion. The reason for this seems to be Apple's fear of GPL3 licensing, which applies to the newer versions of this and other programs. So if you want up-to-date BSD userland components, you need to install them yourself.
As I said, in my case, I used MacPorts to install rsync, but every other package manager available for OS X will have rsync, so use whichever one you prefer. You can also compile manually, or try extracting the copy of rsync that is included with Carbon Copy Cloner: