Man these theories are craazy.
Well, turns out Tenmangu is actually Il Palazzo's second personality. And he took Miwa with him to the ruin, and left Sanshiki (the fake Miwa, the perfected Ropponmatsu) behind to take good care of Shiouji. Given that Sanshiki is a giant pervert, it's likely that she had a replica of Fio's core implanted inside her, just like Excel and Ropponmatsu, and that ended up influencing her personality somehow. I really doubt that's actually Fio who's in control of her, but who knows?
As for what the real Miwa did after Tenmangu's disappearance... I think she helped Piola / Tenmangu make Excel, Hyatt, and Elgala.
This sounds incredibly far-fetched, I know. It's never directly stated, let alone hinted at, but given that in Vol. 16 it's mentioned Miwa is an expert bioengineer (by contrast, Sanshiki took on computing or machinery or something like that, something she's more familiar with) and we know for certain those girls were artificially made, it's not that hard to make the connection.
Thematically, I think it fits.