Do you have any sources to back up this claim? I know for a fact that StatCounter uses JavaScript [1] to collect data, much like Google Analytics. I do not see any reason why they would have a separate collection method for browser statistics. Even if they do have alternative collection methods, if they combine that data source with the javascript collection method - it would still cause FF usage to be under reported.
Sure you can spoof it, but it would be the same for the stat counter.