1. All the hardcoded Unity shortcuts (like Alt+Space, Ctrl+Tab or Super+Tab for example) are not shared with Compiz and the CCSM, so it is possible to double-bind the same keycombinations already used by Unity to other functions without CCSM even showing a warning about it...
2. There are conflicts with hardcoded Unity keycombinations, which are still adjustable via CCSM.
Example: You are unable to change the shortcut for the Window Menu (Alt+Space), although the option is there (CCSM->General->Key Bindings->Window Menu)
Changing the shortcut to anything else makes it snap back to Alt+Space. It is not possible to change the Mouse-shortcut, nor to use Alt+Button3 (Alt+rightMouseButton) for anything else than showing the window menu. Disabling the shortcut is also not possible.
3. If one can not assign hardcoded keybindings/key-mousebindings to anything else and is not able to disable them either, and one wants to use any program that utilizes the same keycombinations/key-mousecombinations (e.g. a game), it would not be possible to play it, because it would always bring up the hardcoded functions, no matter what...
Examples: Alt+Space will always bring up the window menu (window accessibility), Alt+Button3 (RMB) also
1 isn't an issue, since Ctrl+Space and Ctrl+Tab aren't Unity shortcuts. Points 2 and 3 are still valid though.