but it can't make it so that the same modifier key is used for C and V in text editors, and for ^C and ^D in terminals (and XEmacs).
Sure it can. You can re-assign keystrokes for any application using Keyboard Preferences, including the creation of keystrokes for menu items that didn't previously have any.
The caveat is that there has to be a menu item for what you're assigning a keystroke to. Otherwise you'll have to use third-party software to make a macro or rebind.
Though I don't know why you'd want to do something so ridiculous, even if you don't plan to continue using the Mac. I don't have any issues moving between Windows systems and Mac OS, and I certainly wouldn't want to merge the keys used for copy/paste with those used for a break signal in a terminal. Both functions are useful.