I did notice one effect that was occurring when I was towing the trailer...my aero cap rear window (which wasn't secured down) kept opening and closing while I was at speed. This effect did not occur before when I wasn't towing the trailer. I'm pretty sure any gaps at the front of the aero cap wasn't big enough to cause this effect.
Not sure if the gap between the trailer and the truck was causing it or not but I did find it interesting. I've since secured the rear window with magnets...which I can easily remove to see if the effect is still occurring after I install the gap covers.