Soloudinhere, not sure where you shop, but just googling I found quite a few flatbed sellers with various models under $2500. Of course the more options of tool boxes, fancy extras, the more a flatbed will cost. Most have a method of putting sideracks on the bed to contain things well when you need to do that. My flatbed has sides, they come in handy for some stuff, removed for other hauling needs.
Sure folks can buy junkyard truck boxes, along with faded colors, dings from rough removal handling for less money. But OP has a NEW box, bright paint, no dings, so it should sell closer to what she paid from her dealer. Folks replacing box on their newer pickup will not want an older, rough box from a junkyard. More of a “plug and play” item, not needing fixing to use on their newer truck. Heck, her truck dealer might be interested in buying it back for resale to another customer!
You sound like you really dislike flatbeds. Some folks do and that is fine by me. I actually had one lady tell me how ugly they were when I said I liked mine, would never consider owning one to pull her expensive horses with! Thought they were too redneck! But OP is a horse person, wants her truck for trailer pulling a gooseneck. I don’t know anyone who has pulled a gooseneck that willingly goes back to a bumper pull! Better ride for a horse, easier turning, parking, backing, shorter turn radius with a gooseneck than a bumperpull. I would think she plans to keep truck more than a year or two, so resale is not on her list against getting the flatbed. We have never seen a problem getting buyers for a flatbed when it is time to sell them. People other than horse folks or farmers want to buy them for their own reasons.
Just was offering options that allowed her to keep using her present trailer, not wreck the new box sides going over bumps or while turning with low trailer clearance. I would worry about safety with trailer hauling nose high, axles not working as designed. I see many professionals using flatbeds on their farm trucks, both hauling trailers and things for farm uses. Nice lettering on the doors, clean looking trucks, again, very professional looking at the shows even with the flatbeds.