Well...
This is just my 2 cents
(Others on here are "experts" so take it for what its worth!)

Since, the QP is a structural panel...

If you are not going to be installing the new qp's.
My advice to you is to leave the car alone.

Let the person who is going to install the new
quarter panels cut the old ones off. This is regardless
if you are doing a skin or a full OEM replacement.

If you decide to use a skin instead of a full OEM,
my advice to who ever cuts it off would be to do so
below that upper body line.

The line you have drawn is above it.
That line is factory, it looks good, so keep it...
if you are going to do a skin...

If the rear windshield corner is rusted out, I can
understand why you would want to do a full OEM replacement

but if the upper portion (rear w/s corner etc) is good
I would say do a skin....
Save as much of the factory quarter as possible.

This is assuming your body man is good at partial
welded panel replacement.

Best of luck to you either way!