If you store an array return value when using getVariable, it will create a pointer and not a new array. If you use set command for the return value, it will do the same for the variable in the variable space.
I created a repro mission and the hint messages will guide you through it, step by step. {F22508}
Note that the 2nd getVariable returns [-1, "2nd"], so the substraction didn't do anything to the variable in variable space of the logic.
It is possible to bypass this bug by using _variable = +_returnValue;
But it would be better if this is going to get fixed. This is a bug in Arma 2 as well.
If I recall correctly, this is all intended behavior of arrays. Arrays being passed by reference is one of their most valuable characteristics, and trying to change that would break a LOT of existing scripts, to no noteworthy benefit.
The biggest quirk that is probably throwing causing problems for you is how ARMA handles array addition and subtraction. When you do _array1 = _array1 - _array2;, you are actually creating a completely new array in the process, that just happens to contain the contents of _array1 minus the contents of _array2, then assigning _array1 to reference the new array. That's why the variable within the object didn't get changed by the subtraction, but did by the set. Set, select, and resize are the 3 commands that I can think of that for directly manipulating arrays, while addition and subtraction return copies.
And as you mentioned, using _newArray = +_oldArray; creates a copy of _oldArray and stores it's reference in _newArray, and gives you all the functionality you are asking for.
Edit: Relevant wiki article: http://community.bistudio.com/wiki/Array#Changing_an_array
@Hypnomatic
Yes, adding or substracting will create a new copy of an array. I used it to demonstrate that getVariable creates an actual pointer. But would it be logical if...
_var = getPos player;
_var set [2, 1000];
...would suddenly teleport you midair..? :P