yes, time flows the same, but that does not mean that he as transported to 12000BC.
Anyway about this gullible thing about Zeal: sure, they though they could harness Lavos's power. For practical purposes, Queen Zeal did. They just plain didn't like the Earthbound people, so thats why they turned the other way.
I just find it unlikely Magus could get into the highest ranks in Zeal in a week, and get command of the Ocean Palace in a few days.