The windows normally roll down slightly when you ask the door to open itself. It's actually been a thing for a long time on cars with frameless windows, you still need to be waterproof with the doors closed. So if you open the door with the window fully up, it has to slide out from the water proofing successfully. Depending on how tight that seal is, it might not be successful, the window might break. So they normally roll down a bit then open, and when you close it they roll back up to make a stronger seal.

On older cars it was a physical thing that brings the windows lower when you pull the door handle. They could have retained that feature for the manual release, but I guess the added price probably wasn't worth it since the idea is that you only have to manually release in an emergency anyway. So a small chance of the window breaking, like very small, is not a huge deal. If it was every single time you opened the door, sure a chance of breaking the window every day would suck. But for how small the chance is, and only in an emergency, it makes sense to want to save that money.