Did it happen recently? My speaker went all distorted too a couple of days ago right after testing that Philz touch recovery. Although I have a hard time imagening how that would be related....
For what it's worth, my speakers have distorted mildly on full volume for months. I have not installed Philz Touch. It's honestly not hard to damage the tiny speakers in tablets and cell phones, a build up of dust behind the port can cause it. Often times the speakers themselves are cheap and terrible. My wife's tegra note 7 had blown speakers simply from our kid dropping it on a carpeted floor while it was playing audio.
I'm also not sure how the recovery partition would have any influence over the rest of the tablets setting. I'm not convinced the two are related myself. Only way would be if the recovery it's self is improperly flashing software, but for it to be a permanent change that even stock releases won't fix is truly over the top.
Honestly, the TF701 has been enough of a hassle for me for build quality that if Asus released a K1 transformer model tomorrow I would not buy it. Between the now lackluster software support, the poorly constructed docking hinge and other hardware issues combined with their god awful RMA department, I just can't justify it anymore.