My flaps always come out. Hasn’t seemed to affect rain getting in yet. I haven’t paid attention to normal city driving but 100% flaps out on the highway. And yes, there can be a pretty loud ‘pressure reverberation’ with the door windows down. Not always, but not dissimilar to driving a car with one window down. I think it just takes the right speed/wind combination to get the top vibrating at the right frequency. My JK did it as well, but nearly as bad. I am wondering if it’s more an issue with the premium fabric soft top as it is just generally not stretched as tight as the ‘vinyl’ top on my old JK.