Since I'm a builder, I always have tools in the bed of my truck. I don't want them getting wet  in the weather or stolen when I'm parked some place. The bed caps and hard covers don't work for me, since I hook up the GN several times each week.   So I have a roll up tonnaeu cover. When I don't have the trailer hooked up I keep the cover rolled out and in place. When i hook up the trailer, I just roll the cover to the front.  It forms a 10" maybe a little bigger roll. Which I've never had problem with. Granted tool boxes are bigger.  I've seen tool boxes that don't stick up over the sides.  Mainly because I have the cover, I've kept an eye out for products that fit under neath the cover.  Several of the Tonnaeu makers build roll up covers with tool boxes incorporated into them.

I have a long bed truck, with a toolbox that sits over the rails in the front of my bed.  I've had this setup for over a year.  I have a shorter gooseneck trailer, only a 2 horse with 4' SW.  The only time you would be in danger of hitting the toolbox is if you turn the trailer very sharp, and the trailer is on a higher grade than the truck.  I've never run into any trouble with mine so far, but I am very mindful of the situation.  I can see out my back window and watch very carefully.  I try to avoid sharp 90 degree truck to trailer turn offs, unless I know I'm on level ground.  I've been in rough uneven terrain backing in and turning around.  I would think if you have a real long trailer, that you need to make a lot of sharp angles for backing in and out, you might want to take the box off.  If you turn around tight, like a real tight u-turn, is where you have to watch the most.  You wouldn't want to make the u-turn real tight if the u-turn was on a side hill, or unlevel grade.  The gooseneck WILL hit the toolboxes in certain situations. 

My box comes off in minutes just by loosening 2 bolts and sliding out the back of the truck.  I love my toolboxes though.  All of my tools, cords, jacks, straps, jumper cables, tow strap, etc. are always locked in my truck boxes.  With a smaller trailer, the extra room for storage outweighs the caution used on tight turns.  When my toolboxes are on, I kind of treat my gooseneck more like a bumper pull as far as how sharp I will turn the trailer. 

If you want to use the truck boxes, find an area where you can test out your limitations.  That's what I did.  Put the boxes on my truck, went out into the pasture with my trailer.  I had a friend as a spotter to watch the distance between the gooseneck and the boxes.  It doesn't take long to find what you can and can't do with the trailer.  If the thought of having to be cautious with turning is an issue, take the boxes off, or buy one of those gooseneck extender things that people put on short bed trucks.  That will put the gooseneck further back.

Depends on if you have a trailer with a dropped nose or not!  If you have a standard gooseneck it will work with no trouble, if you have a trailer with a dropped nose like most newer 4 STARS or even our Sundowner has, it will hit on some turns.  Our trailer can not be hauled with a 4x4 truck that has a reguler bed because it hits the corners of the bed on some dips in the road or driveways unless we raise the trailer up high in the front.  That is why we have a hauler bed.

Go ahead and buy the truck and sell those side boxes on Craigslist or Ebay or something..... If these side boxes are 5" higher than the bed rail, you'll be in trouble with a gooseneck horse trailer. I got about 9" between my trailer and truck bed and sometimes it almost touches when turning in a driveway. You'll be able to get more for those boxes if they're not all bent up...!