I'm kinda surprised you sprayed over the bed bolts. But as long as you never have to take it off or adjust it I guess it won't be a problem.
It was an option, the place I went to said they usually dont pull them unless the customer requests it and I see no reason I would ever need it off so I told em to just spray em in...... I haven't pulled the bed off my '94 as long as I have owned it (10 years) so I saw no reason to have them standing out. The truck already has a gooseneck hitch installed (that I dont even need) so I didnt see the advantage to having them pull em.