yeah, definitely go with a polyurethane like sikaflex and use a fender washer for more surface area contact. when you penetrate the roof, which is maybe 26ga at best, stick the bolt up thru the roof and then glob a good bit of sealant around the bolt and then drop a fender washer on top of that and then tighten with a nut. the fender washer gives more sealant area and will reduce flex around the bolt penetration. seal good around the threads because water will follow the threads since they are not tapered threads like on pipe fittings.
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have you considered mounting unistrut on the roof? that way you have a fixed and very heavy duty rail that you can attach and detatch items to with ease and you wont be messing with the mounting bolts since everything will be mounting to the strut.
Use this Superstrut Strut Channel Electro-Galvanized Finished to hang conduit and other supports from ceilings. Rust resistant.
www.homedepot.com
you can also make a rack that mounts to the side. instead of penetrating the roof, attach strut to the side of the trailer bolted thru the metal frame and have it go up past the roofline a couple inches and bolt a crossmember. do that 2 or 3 times and you have a nice rack with no roof penetrations. lots of options
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