Arne, I think that second suggestion of yours is a real improvement and I think it's also closer to what Dean was wanting.
I would defer to your judgement, but it seems to me there is still plenty of room for sheetlet spans for the mainsheet.
The beauty of it is, no boomkin is required. (I think a boomkin on that boat, with its long, delicate overhangs, would be unwieldy and would spoil it).
As you say, a rigging cage there would be no real disadvantage, and a safety factor on that after deck, although I don't understand why the mast can't be free standing in that position, or very close to it, even offset if necessary.
I think your second suggestion is an improvement. If it were mine, I would make the mainsail just a little less in area than you have given, and make that mizzen flat cut and with no roach, and put lazyjacks on it. That mizzen will look good and it will "earn its keep".
I suppose you are right, that the keel/rudder arrangement might make a cat-rigged yawl a little bit hard-mouthed when running in a stiff breeze - but with your somewhat higher balance - and also, that is a real pedigree hull shape which ought to pick up a bit more length and directional stability when heeled - I would remain confident it would be good with your suggested junk rig. I can imagine running down wind in a stiff breeze that the mizzen would be furled, and in the worst case scenario there is still the option of adding an end plate to the rudder. For that matter, just lowering a panel and reducing sail area a little is probably all that would be needed if it gets a bit too lively.
(After all, imagine all that over-hanging counter stern was removed - the result would be a transom-hung rudder and a hull profile not so different from your very successful Ingeborg!)
Well done, I say.