If you have an existing barrier coat and it is deteriorating, I could see the need to replace it or at least spot treat.
If there is evidence of osmosis / blistering, I could see the need for removing blisters, drying, and barrier coating.
If the only problem is flaking antifouling paint, sand it back to the gelcoat without removing gelcoat and recoat with new antifouling paint. Beneteau uses vinyl ester resin beneath the gelcoat to inhibit water intrusion and blister formation. You do not need a barrier coat because of the vinyl ester resin. Would a barrier coat be nice to have...sure, but at what cost? You definitely need to ensure that the yard personnel know what they are doing, because they can do more harm than good by removing too much gelcoat.
With regards to the keel.. You need to check the composition of the keel. Some 331's of your vintage had lead keels and some had cast iron for sure. I believe the shoal keels were lead and the deep keels were cast. If it is a lead keel, clean it up and recoat with antifouling paint; if it is cast iron, follow Gunni's advice to blast and epoxy coat prior to applying antifouling paint.
Note that barrier coating is another service / money maker for boat yards. The previous owner of my boat had the boat in Chicago for 5 years, meaning that it was on the hard for at least 6 months every year. When he moved the boat to Charleston, the yard had him do a barrier coat. I am happy that he had it barrier coated; however, I think that it was overkill. The boat had no blisters and with it being on the hard for half of each year, there was minimal moisture content in the hull. I really believe that the yard charged him a considerable amount for a service that was unnecessary. Most manufacturers that incorporate vinyl ester into their lay ups do not advise a barrier coat and doing so may void the warranty on a new boat.