Probably one via Wightlink and the other via Hovertravel
Yes, that is correct.
The cheaper option (prints on a ticket as ANY PERM+HOVRTVL) is for passage on the hovercraft; the higher fare (prints as ANY PERM+WIGHTLK) is for passage on the ferry.
From Brighton, the only fares are Any Permitted, which do
not allow passage on the hovercraft, only on the ferry. Brighton + hovercraft requires a ticket to Ryde Hoverport and then a separate ticket from Ryde to Shanklin.
And from Portsmouth, there are cheaper Any Permitted+Hovertravel tickets which are not valid on the ferry. There are more expensive Any Permitted tickets which aren't valid on the hovercraft, but are on the ferry.
Then from places like Taunton, you have advance fares routed VIA SALISBURY which don't have any mention of a ferry on the ticket and don't even print off a counted place reservation for it.
Simple!