For actual caulk or tube sealant, I would and have used Dicor. Since you are going from horizontal surfaces to vertical, use the non-self-leveling variety.
On my '06 Jayco 1007, I used Eternabond for the top and front/rear ends to cover all seams. It worked really well, made the curve from the roof to the front and rear panels just fine. I used it across the trim strip on the front and rear panels at the bottom that house the gasket
The end result was wherever aluminum roof skin contacted anything else, Eternabond was covering that transition. I've done the same thing with my current PUP as well with only the corner caps on the roof not being covered but I am checking those regularly for signs of fatigue.