Yep, they all do that. And when you're driving around topless the windshield is bouncing around most of the time too. Leaving the rubber weather strip on the frame does help to lessen the noise and problem, but like you said about the opening and closing of the doors, you're going to lose paint over that.
It's worse still if you use a soft top (sorry said hard top first), or worserer still, a bikini top. Both pull rearward on the frame even harder.
Most of us vendors offer at least a kit with short turnbuckle like arms and spherical rod ends ("Heim joints") that mount to a roll-cage and windshield frame bolt hole, to keep the frame forward. BC has, or at least used to have, a longer version that was meant to push forward on the frame from all the way back at a standard roll-bar.
You can make your own of some type as well of course, or you can put up with it. Not all are good options.
The reason this did not come up for some of us many years ago was that when the top came off, so did the doors. Always at the same time, so running wide open and no window frames to interfere with the windshield frame moving around.
And the early models also had removable door window frames. So even if you left the doors in place you did not have an interference issue.
Why a lot of us wanted to convert to the older doors back in the day.
Paul