The actual question is why did Microsoft (and the CDE) choose "Ctrl" rather than the "Alt" key to emulate the Apple settings.
Earlier precedence with MSDOS programs (and with X and Andrew) was that "alt+letter" was far more often used to trigger actions. Also the Alt key on the PC at that time was positioned in exactly the same place as the "command" key on a Macintosh. So it would seem a no-brainer to use the Alt key instead.
I have a few theories as to why ctrl was chosen but I don't really know:
1. CDE wanted to work on machines that did not have any extra key other than Ctrl.
2. Non-PC programs designed for serial terminals had to use ctrl+letter for shortcuts, so they may have thought they were being consistent with this (though they were wrong, as they failed to think of the terminal emulator itself as a program). This may also explain the unintuitive use of shift+insert/del to avoid the shortcut key for operations that were not supported by older terminals.
3. Microsoft wanted existing MSDOS programs to be easily ported to run in a window. Since most were using Alt+letter for shortcuts they used ctrl to avoid interfering.
4. Some foreign keyboards were using the Alt key for typing non-ASCII letters (though was this actually prevalent in 1986?)
If anybody has the real reason, it would be interesting.