Actually to clarify a bit - if your input goals have a tree structure, they all get combined into a single simulation, but the output data will still be structured as the input was.
If the parts of your simulation you want to keep separate are separate in space, this should still allow you to treat them as independent.
Another way that actually does run separate simulations per branch is shown in this scripted example:
https://github.com/Dan-Piker/Kangaroo-examples/blob/master/scripting/CustomIteration.gh
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