Spot welds will result in far less distortion than a welded seam, so my preference would be to use the factory flanges and the spot (plug) welds to hold them on. We had some damage to the upper part of the quarter panel on the wagon. With no reproduction parts available, we lucked out in finding an NOS quarter panel for a 4 door wagon. It did not fit our 2 door, but given all the damage was toward the back of the car, it would fix all the rust issues found.
We had similar issues in accessing the top spot welds that were covered by the next panel up, in our case, the drip rail and roof skin. How to remove the old and install the new.... Our plan was to cut as close to the "spot welded" flange of the original as close as we could, leaving a narrow strip that would be much easier to remove... :
Removing the leftover strips..
The inside of the structural boxing had some strategically placed oval holes that the factory used in spot welding the upper quarter, upper boxing, and drip rail together...
We used this to our advantage in locating the spot welds that would serve the same function once the upper flange of the quarter was back in place....
for minimal deformity, just as the factory had done...
So my recommendation is to do all you can to install these pieces back using spot/plug welds on the factory flanges. Welding on a outward protruding body crease is near impossible to fix once shrinking has pulled it inward. On the ear that mates to the trunk/rear deck filler panel, same thing. Melt out the lead seam and spot weld the panel flanges back together as it was originally done.