There are lots of choices out there. I personally use Dicor on the roof and DAP clear silicone around other areas of the trailer as needed. Lots of discussion online on the use of silicone caulk. I've never personally had an issue with it. Others don't care for it.
2017 Jay Feather 7 22BHM Baja/Andersen WD
2018 F150 4x4 3.5L Ecoboost Max Tow
2015 MB Sprinter 2500 Passenger 2.1L Diesel
2007 Ram 2500 4x4 Cummins 5.9L G56