Ran into this at [[mw:Thread:Project:Support desk/How to get Piwik code into MobileFrontend?]] and, as a result found this comment right above where the hook is called:
// TODO and the suckage continues. This function is really just a wrapper around // OutputPage::getBottomScripts() which takes a Skin param. This should be // cleaned up at some point
Could deprecating Skin::bottomScripts(), and moving the use of the SkinAfterBottomScripts hook to OutputPage::getBottomScripts() fix this?