I have been able to use the modified System application on my own firefoxos-based boards. However, for GPIO I have used a background process based on NodeJS (which exposes the ports using a REST-api). Getting GPIO working on some phoneboards would still prove a challenge as mostly they do not have these easily exposed.
... of the GPIO on the SoC, you only have some of the exposed buttons a device might have. Far from ideal... also, at the moment FirefoxOS itself does not have a notion of GPIO as a WebAPI. But great to see this, nice article.