Moffat found a way to work in Tenant's hand regeneration into the regeneration limits for Matt Smith. It wouldnt be too difficult to find a way to hardwave this
The "16th Doctor"/PiperGate is going both remain an enigma and an incredibly unfortunate burden on the next showrunner to either sort out or ignore. Most likely ignore for the show's health but then do you start with a new "16th" or jump to "17th"? If so, WHAT happened there?