Cutting with the overlap allows a perfect gap. I have not used them yet, but cleco clips can hold the joint areas together with the right gap for butt welding. Use sheet metal screws to hold the quarter in place until it's fitted. Don't tack weld until everything is exactly where it belongs.
On my car I chose to keep the passenger quarter and just use an extension and patch for the outer wheel house. My brace under the tail panel is in excellent condition, so I will not replace that and the trunk will just replace the bottom pan area. I cannot imagine all the work required to disconnect it from the frame rails, rear valence brace, and in front where the seam is with the floor? I have a vert and more room to work with. As you can see from the pics, I do not see how you will fit a complete trunk without the tail panel off. Excuse all the junk in my trunk LOL.
I am going with the original color vedoro green. The idiots who did the previous work slapped an extension over top of the original quarter to conceal the rust and used a generous helping of bondo to slather and hide the rest. The welds were not done properly either and could be picked apart with a screwdriver. WTF are people like that doing working on cars? Ok, enough...I am fixing it the way she deserves.