Sorry if this has been covered before, but if so, I missed it.

Why do the underwing stores of the F/A-18E and F toe outward? Is it a
clearance problem, or a separation problem, or...?

They don't, at least in the photos I've seen.

Maybe you saw a couple of shots taken with a wide-angle lens?

They do toe out. IIRC, it's a separation problem. It's also a humongous
drag problem.

R / John