The Xcode SCM comparison window in Xcode 3.0 is not yet as full- featured as the comparison window in FileMerge.
Much more is planned, but for Xcode 3.0, it is primarily meant to be an in-app convenience for looking at SCM diffs, not a full-featured, integrated editing environment.
For one, unlike in the refactoring window (which is the other place this UI is employed in Xcode 3.0), you can't edit the contents of the right-hand side other than by flipping arrows.
For two, the window does not represent the original file in the way a regular Xcode editor does. Under the covers, the documents on the left and right-hand sides of the window are actually temporary files. This is why Cmd-S doesn't work, and why modifying the contents of the right- hand side document by flipping arrows doesn't affect the original text file.
To save the right-hand document in the Xcode SCM comparison window, go to the File menu and hold down the Option key. You'll see the option "Save a Copy As", with the keystroke shortcut Command-Option-Shift-S, become active. (There is no way to save the left-hand text contents, other than by copying it and pasting it into a new document.)
It's unfortunate in this case that "Save a Copy As" and "Save As" were combined into one menu item, with the latter being the default option shown, because only the former is possible in this window, so it's not an easily discoverable option. The Xcode documentation will be updated at some point to describe all this.
If you want editing and comparison combined, you should probably switch back to using FileMerge for now. This option is available in the Xcode preferences window, SCM toolbar icon, Options tab, "View comparison using:" popup button.