Emet's task is a fairly significant one. If someone gets appointed to the Convocation, that's a lifelong post. It's always significantly easier to get someone in than it is to get them out, and the last thing that you want to be doing is spending the rest of your career working around a prospective colleague who is unreliable or is at odds with you. That's why small, influential groups of people like these tend to become progressively more conservative and homogenous over time (although nepotism is a contributing factor to this as well). Emet genuinely thinks highly of Hermes for his ability to follow through on the decision to eradicate the Iykaones, and directly states as much immediately following the cutscene:

'...I don't know what answer he's searching for, or if it is within our power to give it. But I believe he would make a fine Fandaniel, and that if he rejects us out of hand, we will all be the lesser for it.'

On the subject of soul transference, I think the hint lies in 'Through His Eyes'. The Phoinix demonstrated that a drifting soul burdened with regret could accidentally merge with a Creation to resist the pull of the Underworld. That's effectively the basis for the hemitheos, Zodiark's heart, and body hopping right there. Once Lahabrea saw what happened with the soul hitched on to his Phoinix, he likely would have figured out how to do the rest.

As for the souls themselves, they're not unique entities. They store your memories while you're alive, and then go to the Underworld to be cleansed and used by someone new. Sometimes that process is imperfect and the inheritor of a soul retains memories of a previous life. In Amon's case, Hermes soul had previously been blasted with aether from Kairos, which left the memories from Elpis etched on his soul after being cleansed in the aetheric sea. Normally, you're supposed to use the Convocation job crystals instead to regain your 'lost' memories.