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We saw from Frankenstein humans animosity against nobles stems from the fact that noble's contracts which gone rampage. Before becoming a butler, he was the champion of humanity. So it would be obvious that they unite under him. Sixth elder could probably be one of his students when he was still experimenting. And the unearthed site could be Frankenstein old laboratory which he closed when Rai sealed his power.
I seriously doubt that. It would be too much of a contradiction of what we saw until now. For example, Lukedonia would have never accepted Frankenstein if he was behind the Union, and it would also mean that all the goodness we saw in him was just a facade... a mere act, like his devotion to Rai. So... nope: It wouldn't make any sense to me.
The only way Franky helped the Union was by letting his old notepad unguarded, thus letting Crombell find it and take advantage of Frankenstein's research. But I can hardly see him as responsible for such a development.
I wonder if in its creation, Union was originally good. Good, as in, to mediate the relationship between nobles and humans. They used to have bad relationship as far as I can remember, I think, although after changes in leadership the nobles got more towards assisting the humans but still hiding themselves from the public. If that is the case then I can see a probability that Frank might play a part in it. Although later on he went against the nobles because they attacked humans(?) (not sure about this, I forgot about the flashback of Frank's visit to Lukedonia).
That being said, I believe Union evolved more because the traitorous nobles and the notes Frank kindly left for Crombel.