>In a newspaper combine, you stack up, two beehives with a sheet of newspaper in between (with some small cuts in it),to avoid the hives fighting it out, Correct?
Yes.
>One remedy for a hive with laying workers is the shake-out. Why doesn't that start a bee war, when they try to enter a different hive?
They are probably killed if they don't arrive at a new hive bearing gifts....nectar and pollen.
>There are times, when two queens live together in the same hive (mother/daughter or sisters).
Yes, but it's usually a temporary thing. Eventually, the young or most prolific queen will usually be the only queen.
>Lastly, there are those towers with two boxes (side by side) each with its separate queen (and excluder), with the workers happily (?) coexisting.
In my experience, in the spring and summer this works, but I have found situations where the second queen is being balled in the fall. My experience is with two nucs in a 10-frame box with a queen excluder on top of this box and boxes full of honey frames above this for common feed.
>Could someone explain what I'm missing?
It's kind of like people, if you have something that can benefit another person, they like you. If you can't offer anything that person needs, they don't need you and they'll like you less or not like you at all.
Hope this helps,
Steve