as far as i know and believe only tickets routed HOVERTRAVEL are valid on the hovercraft.
This was the case was i went to the Isle of Wight 18months ago, so yes i'm sure a route excess would apply in this case.
This taken from Hovertravel's Website :
IMPORTANT : Please state 'Ryde Hoverport' when purchasing your tickets to ensure you are traveling via Hovertravel. If your ticket states 'Ryde Esplanade', or any other Island destination, then your ticket will not be vaild to use on Hovertravel services.