While a command is running (tested with a pause or TTS with "Wait until speech completes before continuing command" checked), it's impossible to close to command list, either by clicking "Done" or "Cancel", unless said command has "Allow other commands to be executed while this one is running" checked.
Other buttons remain functional, commands can be created, and the "Confirm Close" dialog pops up if anything has been modified/added when "Cancel" is clicked, but the actual command list window will only close after the command has finished executing.
Regardless of there being an underlying reason for keeping the list open, providing no feedback(such as a simple "Please wait until commands have finished" dialog, possibly with a "Force stop" option) is potentially frustrating for a user that isn't aware of this behaviour.