AFAIK, rear quarter panels are hardest to replace because they are spot welded in. Unlike doors, trunk, hood and front fenders which are bolt on.
A unibody car (boxster) may not be that easy to just pull out all the damage. However they pull out the frame, the car will not be as strong as it was before. Take an empty soda can. Crush it, then staighten it out. The result is the can is weaker than it was before (on the whole). Same with the car, the creases in the metal are still there, perhaps more shallow because they are hammered out, or in some places cut out. Point is, once the structure is stressed again, chances are it will fold along those same wrinkes with less force. The question is how much damage can you live with? What difference does it really make? Practically speaking, probably none.
Having said that, if it was me, I would not want a new rear quarter panel unless I knew for certain the work was top notch and damage to it was extensive (deep creases). It requires a lot of work and care to do right. Much more than some bondo.
A replaced quarter is easier to spot on resale, seam sealer and rust proofing is rarely as good as OEM, and not many shops have comparable resistance type welders $$, and will most likely mig plug weld it in.
As for paint, where it is blended in usually cracks/crazes/discolors over time because it is thinnest there (less UV protection, and impossible to prepare well enough for optimal adhesion to substrate, etc...). It's better to do the whole panel, than blend into one. Most likely only you will know the difference, if at all.
If the chassis is still square, that's the most important thing. That would be my primary concern. Secondly, as far as the re-spray, I would push for a real good match, perhaps having them shoot a test panel and let it dry (paint looks different when it dries and under paint booth lighting) and have the shop not blend into another panel if possible. Metallics make matching even harder. In the end, relax. We can't keep these cars new forever, though we all would like to. Fix it best you can, and drive on. You'll feel much better when you get it back on the road.