Just for clarification...the FastCat terminal is at Portsmouth Harbour, whereas (I believe) only Hovercraft tickets are issued to P&S (then shuttle bus to terminal)
All tickets to Shanklin are routed via Portsmouth harbour and the Wightlink Fastcat service to Ryde Pier.
The through tickets on the Hovercraft are specifically to Ryde Hoverport. The hoverport is over a footbridge from Ryde Esplanade Station and the bus station.
If travelling by Hovercraft there is a connecting bus the Hoverbus which goes from Portsmouth and Southsea station to the Hoverport and returns via the hard bus station which is next to Portsmouth harbour station to Portsmouth and Southsea station.
On the fast cat you just use the rail tickets, on the hovercraft you go to the ticket desk at the hoverport and they make a reservation for you on the next flight and ask if you want a return reservation.