It comes in its own mod folder (well you need to manually create the modfolder first) like most other mods, so its fully independent unless you add files to it.
I'm not sure if you need the GUAO though as I did unlock most of the unavailable units in it by default.
Re Retrofit, I have my own unit balance, so the only thing it might add are the siege things. Would involved some manual text edit by you to implement them I suppose.
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