For fix this behavior we just can add out = {} before our code. Ok.
However I can not imagine the situation when such behavior would be useful.
It's mostly historical thing actually - that's how "out" worked in previous LuaCombinator mods, so I just copied that familiar behavior from there.
Can be useful if you process and output many signals, so that you don't have to explicitly set them all every time.
And I tend to use it as a state too, as you can see in examples in the mod description - e.g. out.stone = out.stone + <something>
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Such things can't be easily changed in this mod at this point, since it can obviously break all existing uses of it, unless enabled via some option, and as you mentioned workaround is pretty trivial, if you need the thing cleared before code runs.