Spacious does not use any private system interfaces. Instead, it implements its actions by simulating the key presses that the system assigned to specific functions (like switching Spaces).
If all key presses are captured by f.ex. a virtualization solution (like VMWare Fusion, Parallels Desktop) or a game, before the key press reaches the system itself, the simulated key presses can't reach the system either. In consequence, the desired function is not triggered.
For some actions (f.ex. Mission Control) Spacious can work around this by launching the Mission Control.app in the Applications folder. For all other actions, however, this is the rule of thumb: Spacious can trigger a function whenever you can also trigger it via your keyboard. If you can't trigger it via your keyboard, however, Spacious also can't trigger it,