I just finished one side install of an AMD quarter panel on an A-body (nice fit and quality, but that's not for this post).
I have stripped off the black electrocoat from the exterior before spraying epoxy primer. I am going to use 3M body Schutz on the inner of the quarter panel to give it a factory look. Do I need to remove the electrocat before spraying, or am I ok to go over it in this case?

I think you can just scuff it and spray over it.

I bought a car that came with a new repo hood that was coated, and it got lightly sanded and then primed and painted with no issues.

Why would you want to strip off the E coat? E coat is a better corrosion preventer then any spray on primer. Don't strip it off. Not even on outer side of panels. Just sand it prime or seal and top coat.

I'm not sure I agree with that, but for the inside it doesn't matter I have left cars sit out with just ecoated panels and after a year or so they rust. Where cars I epoxied and left sit out, just some fading. I'd scuff it good and coat it.

The point of E coat is not to let it sit out side unpainted. My point is why would you strip off the E coat? You just sand it prime or seal it and paint it. Every new car built in the last 20 years is E coated sealed and painted. You don't see newer cars rusted out in a couple of years like you used to. I've been doing body work and paint for 35 years. We never strip off E coat on new parts unless there junk made in China aftermarket. And we only use the aftermarket on older cars when insurence companies won't pay for OEM.