You will likely have to ride out some weather at anchor at some point and there really is no substitute for all chain at that point with a good snubber. When it gets really bad, the chafe resistance of the chain becomes crucial because even a good snubber can fail. I would think that you would want the ability to anchor on all chain with good scope in all reasonable depths(up to 50'). So a half keg with some additional heavy rope rode would be my choice, the additional rode for when it is super deep.
As far as putting 200' of chain on your stern anchor, that will make it very hard to use. It sounds like the chain won't fit your windlass and that would me re-leading it forwards anyways. Much more than 50' or so and it will become unmanageable. If you have the choice, storing this closer to the centerline of the boat would good. Up to a reasonable point, weight on a boat isn't too bad but the issue is having it in the ends because your inertia will increase which will put the boat out of phase with the waves. In extreme cases, poorly loaded boats pitch wildly. Since you have already been carrying the weight of the primary anchor and chain forwards and haven't had problems, I wouldn't worry about it but it is a considering when packing.