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I don't think you'll have an issue with a goose neck as far as clearance goes- unless your gooseneck is boxed all the way up the hitch, which I've never seen before. Guys that tow a 5er with a short bed can use a swing hitch, which I believe swings out to make a turn without crushing your cab
The gooseneck allows for more wiggling, more clearance, and more wobble, making it FAR prefered for offroad travel. The fifthwheel doesn't allow any tilt (standard ones... you can get ones that do allow tilt) making it more stable.
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My turn over ball Cody hitch is rated 35K. You can see the difference in the twisting and turning the gooseneck hitch can handle when you pull a trailer through rough pasture and across ditches. I don't think any 5ft wheel could handle the differences in the angles of truck and trailer that a goosehitch can. I see a lot of short bed trucks pulling horsetrailers etc. with no problems. Some of the goosehitches allows for a 6" inch foreward of the rear axle for long bed, while in the short bed the ball is installed right above the axle.
The only problem with a clearance issue on a shortbed is when I've installed a gooseneck adapter on a 5W trailer. They make offsets to help correct the nose/cab clearance problem which works out okay most the time. The biggest problem I've seen was on a 5W with an extended pin box (which is pretty common nowadays) the back of the pin box will get into the bedsides with a gooseneck adapter that has any offset. The only to remedy that is a no offset adapter which creates the nose/cab clearance problem. just gotta pay attention when you're turning.
As for the fifth wheel vs. gooseneck I think a 5W is more stable andeasier to hook up. and as far as the weeble wobble of a gooseneck unless you just buy the cheapest hitch you can find or have something old, most 5W hitch heads pivot on both axis's.