It would be nice if the magazine was a proxy in the weapon p3d. Currently, as far as I know, the magazine is "hardcoded" in the p3d and isn't changed depending on the magazine being loaded.
Since magazines in CfgMagazines have a "model" config entry, it should be possible to use that as source for the proxy, i.e. no other configuration entries would be required.
Simply add a "/a3/data_f/proxies/weapon_slots/MAGAZINE" proxy to the weapon and your done.