I think it’s much easier for players to accept that they are prohibited from invading the same space due to their separate turns like in the standard games. If you tell them instead: “you can’t do this due to balancing reasons†most of them will start to argue. Especially when you present them rules you’ve invented by yourself instead of the original OOB rules. At least that’s my experience concerning house rules; no matter if you are talking of tabletop or board games.  :wink:
Shure, the allies had their difficulties working together – if you think of Generals like Patton and Montgomery; or the various discussions about the distribution of resources – but if you look at the differences inbetween the US (or Japanese) army and navy, you also have these troubles within one nation itself.
With your examples you’ve nearly give a nearly complete list of the whole western allied campaign to liberate Europe from 1943 onward. I think this is a little bit more than a few examples. Sure, they had their troubles, but in general they were working very effective together; especially concerning the grand-strategic level A&A tries to simulate.
Maybe a better way to smoothing the game a little bit and to eliminate “can-openers†would be two combined turns per game-turn
a) for the axis in Europe a combined German/Italian turn (as you’ve stated correct, the various axis nations in Europe (Italy, Bulgaria, Hungary, Rumania and to some degree even Finland) needed German assistance).
b) For the allies in the Pacific a combined US/ANZAC turn (since they coordinated their naval operations e.g. the campaign for the Solomon’s).
I wouldn’t include the British Pacific forces into this allied combined move, you prevent discussions why they can’t attack together in the European TOW and btw. the UK-Fleet in the Pac is no match for the IJN and there is no money expand it or rebuild it once  it’s gone.
In general I would say: if a system isn’t broken, don’t fix it! (And I’m not sure the system “turn-order†is broken.  :wink: )