If Structure1.structure2.list is a Handle Class, you can assign to another name (myList) and modify the original object via myList. This also makes the final reassignment unnecessary.
Another option is the workaround you mentioned.
As another option, you could try pulling the logic dealing with myList into a new function, where myList is both an input and output.
This (with some caveats) should pass Structure1.structure2.list by pointer, or directly inline that function without a data copy.
The caveats are that a copy is generated when it is unsafe to pass by pointer. For example:
[x,x.f] = myfun(x,x.f);
Within myfun, the input values are distinct, so if one is modified, the other should not be. Thus one of x and x.f must be copied before calling myfun.
