It is probably that SI have only restarted the Bournemouth route because of financial incentives offered by that airport. However, fares undercut Southampton but frequency is of course less.
When they say 'journeys are via Jersey but begin and end in Guernsey', that is a nice way of saying that they are only flying to one Channel Island and if you want to visit the other one then you can damn well use their indirect route.
One of the Jetstreams is off for maintainence at the moment so depending on popularity perhaps frequency will be increased next summer.