Reading the description of Liquipel it says it permeates the whole device... i.e. it enters all the ports and coats the guts of the iPhone.
I'd suggest you contact an Apple store and seek their opinion. I'm guessing they would say it voids your warranty.
I see no endorsement from Apple on the Liquipel site so 'buyer beware'.
Liquipel's treatment doesn't require any alteration or even opening the device as the nanocoating is applied without opening the device itself and is drawn into the phone thru the existing ports. I've taken in my treated phone and had no problems getting it replaced each time I've had an unrelated issue.