Silicone is a bad choice to use on the outside of a rig. The best choice is to use what Winnebago uses where the roof meets the side walls. It is thermoplastic called Kop-r-lastic from the Canadian based company Henry. Available from Winnebago only for $18 a tube. I guess the company has the same product HE212 available at Home depot & such for $9 a tube. I haven't found it!
If water should get in , my guess it would show up on the headliner or where the sun visors are attached As stated earlier, it does sound like there is too much movement.