For any welded patch panels I think you have to get it squeaky clean and put epoxy primer on it and then good paint over it on both sides. I see lots of guys with patch panels and primer driving around for months or years and it fails before it even gets paint put on it due to getting wet too many times. Also the welds have to be solid with no porosity. You'd be surprised if you stick a flashlight up to what appears to be a solid weld line and see light poke thru in spots that are easy to not see at a first glance. You have to weld panels on one dot at a tie and it's easy to leave super tiny air gaps between the dots and that is where your rust is going to start first.

On the spot welds you'd have to weld up any that did not stack over the new panel holes and seal them up first. I'd be surprised if they were all in the same location, but if it was done with robots it may be close?

Those trim nail studs that some mopars came with I think you can buy those and put them on with an autobody stud gun?

It's going to look better splitting the color with trim. You could always put a thin pinstripe between the two colors if there is no trim to make it look better. Rust under trim comes from trapped dirt so if you hose it out and keep it dry and clean it should last a long time if you have good quality paint on it.