Yesterday, I mentioned that OS X 10.9 Mavericks wasn't remembering the key mappings for my PC keyboard. Since then, I chanced upon a utility called KeyRemap4MacBook, dubbed "a powerful and stable keyboard customizer for OS X".
Buried in its inexplicable option list, I was able to find Alt/Command and Windows/Option remappings, as well as a few other tricks. Best of all, it remembers the mappings after a system restart, and when the keyboard is removed and plugged in again.
It still feels weird using a third party utility to compensate for a feature that's supposed to work in the base system, but for now it's a solution and I'll take it. Thank you Takayama Fumihiko for saving me much frustration!