Yes, I would agree with you on this point. Whatever activities the godlike alien would be doing on earth would largely largely confuse the heck out of us (though I'm sure that Reed Richards types would quickly puzzle it out). Also, even if we did figure it out, I'm not sure we could do much about it.
Just last night I was reading the story where the FF have to release Galactus's menagerie, in order to simply get his attention.
I think that true godlike aliens would be much more Lovecraftian, in their interactions with humans. We'd either be something they scraped off their boots, before jumping back into their gigantic space ships, or we'd be meat snacks.