Hi Geoff,
When I want to remove a panel, I either use a spotweld cutter/drill (there's different types) or grind the metal wafer thin at the spotwelds so that it can be prised free without distorting the mounting flange.
I've had bad luck with the factory applied primer on replacement panels. One body expert told me it was only to prevent rust on panels in storage/transit.
I remember removing the old beige primer that original Fiat panels came coated with and finding little spidery lines of rust underneath!
So unless the paint used is a modern etch primer, I think I'd play it safe and remove it. Seeing as you've stripped all the other panels and will be doing a full respray, it would be calamitous if the black primer? failed later.

I'm curious as to why you decided to replace the rear quarter panel rather than repair the damage, didn't look too bad to me, or am I missing something?
Best of luck with the rebuild,
Al.