Half an hour or so of hacking gave me this solution:
Whenever an unrecognised key is pressed, the above popup appears listing the current controls. Pressing a known key causes the popup to disappear.
The reviewer had a legitimate complaint - the controls aren’t obvious. Hopefully the ability to change keys via the Preferences menu option mitigates that, and the new popup should encourage players to have their fingers on the correct keys when the game starts up.
I’ve submitted SFE 1.4 to Apple. What’s infuriating is that the update will no doubt languish in their approval queue for the next month.