Some of the top shapers (McTavish, for example) licensed their name to bigger companies, or licensed the use of a particular board shape. But the shaper will continue to make their own boards.
For McT, the GSI boards are usually expoxy/SLX while at the McT factory its all hand made PU and generally custom built. So the licensing is given for some extra money for the shaper and the shaper continues to work in a more exclusive higher value range.
As is usual for surfing, there is a bit of snobbery and few people would recommend the GSI McT boards over a 'genuine' McT, although they may well be exactly the same board apart from (and this is an important 'apart from') the different material. See the discussion here http://www.seabreeze.com.au/forums/Surf ... -the-same/
. I couldnt tell you whether these views are justified; there is a culture of 'anything hand shaped is better than from a factory' regardless of the truth. That said, given McT's reputation I would think his hand made boards are top quality without a doubt - but at a much higher price.
However, the shaper's current involvement with GSI is most likely (I have no inside info) essentially walking to the mailbox to collect a cheque. So in that respect there is no real link between what McT produces himself and the ones GSI produce with his name. I doubt that McT runs his eye over the GSI products.
I don't know about Channel Islands but its possible they licensed the board because GSI is simply a bigger player and has a much wider global reach than CI; and again they just walk to the mailbox every month or so.