Yes, I was able to successfully install the add-on files from the Sparkfun product page, such that when I programmed it I was using that specific board in the Arduino IDE.
The note for this mentioned: “As of June 19, 2012 these boards will be shipping with a slightly modified version of the same bootloader included with the Arduino Leonardo. It’s modified to use our own VID and PID”
My thoughts: if the bootloader really is a copy of Leonardo’s but with a new VID & PID, then I don’t see why the two boards are behaving differently for me. But, maybe there are other changes in the bootloader itself that require extra PWM configuration (to disable them)? I haven’t gotten into these files (and in fact, would have just bought a breakout board had I been willing to do so), but I can try messing around with the internal registers myself if that’s the case.