Don't they say you shouldn't fully submerge the phone in water? I know in the demonstration they showed that but I think I remember hearing or reading them saying they don't recommend that.
Of course you shouldn't fully submerge your phone in water, even LiquiPel'd. Just like you shouldn't slam headlong into a cinder block wall in a car going 80 MPH, just because you have seat belts and airbags protecting you. Or how you shouldn't put on a bullet proof vest and then deliberately get shot in the chest, because you trust the vest will protect you.
Liquipel is to help protect against accidents, but is not an ironclad guarantee that your phone will be fully protected against every dunk. They don't recommend intentional dunking because they don't want idiots coming back to them complaining that their iPhones died when they repeatedly dunked their phones in water to "test" the LiquiPel. At the very least it's a liability disclaimer, and at most it's common sense that you shouldn't tempt fate.
Anyway, back to the topic: if it were me, I'd consider that toilet-dunked iPhone a total loss, go to the Apple Store and be prepared to plunk down money on a replacement. I'd even put it in a ziplock bag and make the genius fully aware of where that phone has been before he or she opens the bag up and attempts to handle the phone.
Because, call me crazy, but, that phone has been in the same liquid where human waste is routinely deposited. I don't care how thorough a cleaning it gets, that phone would never touch my face again.
And if I were the Genius handling that case, I'd appreciate being warned before I go mucking around with a phone that's been submerged in toilet water. I might even do the freebie thing if it were within my power to do so, if the person were honest so I could get the Purell at the ready.
(That's also why my phone and other gadgets are banned from the bathroom... to avoid the risk of them taking a "bath" in there.)