The information about the DevKit speaker pins being shorted is not widely reported, but it was given in the DevKit Hardware topic under Piezo Speaker:
Two pins, A2 and A3 directly drive a piezoelectric element inside of a
small black plastic housing. Caution there is no circuit protection
these pins: Theoretically there could be some problems with driving both
pins as outputs, we suggest configuring one pin to input. In practice
this has not caused any issues to date but please comment if you have
Unfortunately, the Arduboy library and some of the included examples still have this problem. Fortunately, the ATmega32u4 processor used in the DevKit (and production Arduboy) seems to be robust enough not to be damaged by it. But in any case, it’s not a good idea to do it. Also, it’s good that this isn’t a problem with the production Arduboy.
In the next day or so, I plan to make fixes to the Arduino library V1.2 code to address this problem.