3 problems after drivers door repaired/replaced

The only way to know where to put the blame is to have the causes diagnosed first. I've never owned a vehicle with all kinds of toys and gimmicks, and I never had to work on them at the dealership where I worked, but I can offer a general observation. There are going to be switches involved on the body or built into the latch assembly. Those will relate to the anti-theft system. When you have headlights that turn on automatically, you know there's going to be a computer involved. Computers for things like this are, in my opinion, an inappropriate use of technology. They are inherently unreliable and trouble-prone, and they live in an environment that is hard on electronics. When you have multiple symptoms all related to the same computer, the Body Computer in this case, those computers are pretty hard to damage in a crash, but it IS fairly common to blow fuses.

Also, if the battery needed to be disconnected during the repairs, fuses commonly blow when the battery is reconnected, from the current surge. Start by checking the fuses inside and under the hood. On most cars the power windows work without a computer because that is a safety issue. It's the "automatic-down" you're referring to that adds the computer to the circuit, and that's the part that isn't working.

On some car models that feature is built into the switch assembly. The mechanic may have installed the switch from the used car, and that one perhaps didn't have that feature. In that case it's just a matter of installing your original switch.

I'm not so sure a blown fuse would be responsible for the headlights not turning off, but when a computer is involved, each car model does different things when one is blown. Most commonly things don't work at all. Getting back to the door switches, if one is broken / misadjusted / disconnected, the computer may be keeping the lights on because it thinks the door is open and you're still unloading stuff. Some cars use auto-adjusting switches, and slamming the door really hard will over-adjust them to the point they don't turn off when the door is closed. That used to be a problem on Dodge Caravans and it had a real easy fix. Yours has a rubber seal over it so I can't tell if it is of that type. First look on the "B" pillar, (the rear of the door opening), for that switch. Be sure the bolt is tight that holds it on. Next, see if you can pull that rubber boot off to expose the plunger. If you don't know what it looks like, you can find a photo of it at the Rock Auto web site. If you can post a photo with the boot off, I can tell you if being hit could have over-adjusted it, and how to fix it.