Remember, a gooseneck hitch is a ball located on the bed of the truck. It doesn't sit a foot to 18 inches or higher off the bed of the truck attached with rails and such. Many gooseneck hitches are designed so they can be flipped over or removed easily, thus giving the truck bed 100% usability when not towing.
Folks towing horse trailers use the bed of their trucks for multiple reasons. Thinking of one immediately ... moving hay and straw bails to the barns and fields. They need the full truck bed as their use is for more than just towing a trailer for recreation.
Horse trailer goose necks have been around, seemingly ... forever. Part of it (today) may be ... well ... that's just the way it is. The basic original design works so well... why change it?
That's the advantage of a gooseneck. (I know, I've lived in farming country, pretty much all my life, except for a jaunt with Uncle Sam living in tents for a while).