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I would have assumed the former but I just don't know, I'm sorry.
The only time I can imagine this would matter is if you have multiple mods that modify the same thing - which sounds like a bad idea in any case! Is that the situation?
A short guide to Stellaris mod load order, which was inspired by ShadyDemoness and his quite unique The Great Plan II mod anthology (offline). Be sure to keep in mind, that PDX often changes rules