I want a nylon rifle case that has some kind of room for a pistol, but also has webbing on the outside that I can attach mag pouches to so that I can remove them and put them on a belt.

Ideally I'd prefer a chest rig that can be mounted to the outside of the bag, but I figure this will be a close approximation.

uhh..i'm confused exactly what you're looking for, but hook and loop strips can be sewn almost anywhere and are readily available in different widths/strengths..maybe concentrate first on a weapon case that is large enough to hold your rifle then check out the large variety of separate cases/holsters that could be hook and loop mounted both inside and outside the weapon case..not sure that this helped, but i tried  :)

How about this?  You could attach any molle accessories, such as a pistol pouch, as well as mag pouches, whatever.