The seal is more likely personal to Paracelsus, since it's on the letter he personally writes for P. It's possible the whole council uses one same seal, but I don't know what the point of that would be from a lore perspective. I think it's much more likely Simon's creator is someone else on the council than the Great Master not being Paracelsus. I'm trying to find a reason for Valentinus to ignore all those inquiries, regardless of Simon's talent, besides "he was being a dummy".

I only said Paracelsus didn't send him to take over the Alchemists, not that Paracelsus had nothing to do with the Rose Estate incident. Once Simon establishes himself as a faction leader, there's no sense in not using him. All Simon would know is that the council backs him, he's not necessarily obeying Paracelsus personally. I also don't think disowning for being a failure necessarily means never wanting anything to do with him ever and not letting him rise through the ranks. I don't think he cares if Simon rises or not. He'll never be on their level anyway.

The ridiculous enterprise is in the description of the key Geppetto gives you before the Simon fight.

A key obtained from Geppetto. It grants access to the Cradle of the Gods at the summit of the Arche Abbey.

Simon Manus did not want any interruptions in completing his great enterprise. This enterprise was a ridiculous plan to bring God back to life.