with all due respect to MC, i had exactly this same problem, of an old pickup truck and fixed it the same way as described by the place you took it to.
i would get out of the truck and close the door by grabbing the door and slamming it shut. also when opening it i would grab the door by the upper part of the window frame and give it a tug to open it.
eventually these repetitive door pulls, slams and whacks deformed the doors so they leaked.
i did exactly what you describe and “re formed” the doors to close completely and weather tight. the only difference i did, was to completely roll the window down so it was NOT in the upper part of the track.
i dont mean to be critical here, but… by any chance does a regular user of the car have a habit of grabbing the window frames and either lifting out of the car, or lowering into the car while hanging onto the window frames? that sounds like what is contributing to this problem.