The techs are probably baffled. This is not a common problem. Are they charging you for this work or is it being covered under some sort of warranty? This sort of work is mostly labor and could get expensive.
There should be a plastic liner, often called a “shower curtain,” between the metal door and the inner door panel. This plastic liner is designed to keep the inner door panel from getting wet when water inevitably gets into the door. This liner would have had to be removed or cut to access the lowest parts of the door, where the water is pooling.
If the inner panels are the source of the mold smell the plastic liner is not doing it’s job.
I’d want to examine the inside of each door before they reinstall the inner panels to verify that all water is gone and that the inside of the door is clean, dry, and free of mold.
Maybe you’re not inclined to do it, but if this were my vehicle I’d be taking the door panels off and checking out the insides of the doors for myself. If they’re holding water there’s a problem.