I used to use an elastomeric coating on my old campers/trailers when they were aluminum roofs. I put it on the "raw" aluminum and over seams, flanges, etc., and it worked really well for many years (I never used silicone.) It also did help keep the rig cooler and quieter when it rained. That was 20 years ago though, and with today's new roof materials I think I'd most likely stick with what was recommended for your roof material specifically. I do remember that when I had to replace a roof vent I had to cut around the flange to get it off and replace it, then I had to clean the whole area around it when I reinstalled and re-coat. It doesn't come off easily!
Just my experiences.
Dak