Another vote for Eternabond. I hated the skylight in the bathroom. I took it out 10 years ago, placed a piece of plywood in it's place and then put 6" Eternabond over that overlapping each piece by approximately 1". Painted it with the UV paint from Eternabond. Haven't touched it since and still holding as well as it did the day I put it on.
I also had a roof leak(s) where the endcaps met the rubber roof. After I made my repairs, I covered the joints with 6" Eternabond and UV paint. Again, no problems since.
Based on the quality of trailers and my experience with endcaps, the first thing I do to my next traile will be to cover those joints with Eternabond as a proactive measure.
I keep some extra Eternabond in my trailer for the "oops" situations while on the road. Haven't needed it yet, but glad it's there.