I assumed as much.
It's just odd they'd put that behind hex coding. Most of what's behind hex coding is... pretty unimportant; the Knave of Hearts and Hansel and Gretel both feature lots of dialogue in hex, though it's nothing more than faux-philosophical musings like we get from the Puppet units in the Bunker. The Compound and False Idol both feature hex subtitles that are informative, but that's just about it.
Her Inflorescence's dialogue is otherwise... pretty suggestive in terms of narrative, but the hex dialogue having no real impact is kind of perplexing.
I don't see why waking up Zodiark wouldn't be part of the plan, assuming Zenos doesn't just go up to the moon and snatch him before everything goes to Hell in a handbasket. Zodiark is way too big a factor for Danny Boy to leave unaccounted for.