To me, Gotash's reason for obtaining the prism seemed to be first, controlling a potential threat to the plan and second, finding out more. I think it's Balthazar who describes him as having the mind of a scientist. As such, having knowledge of the prism must have prompted action.
As for why Gortash would have picked the Emperor to steal the prism, I can offer nothing but speculation based on my memories of BG3 and the old TSR/AD&D books. Let's take your standard mind flayer. They are being described as having some individuality, but at the same time sharing a deep connection with their elder brain. It was quite possible, though, that a standard mind flayer gets disconnected from that connection due to distance, magic or other things. These disconnected mind flayers would not revert to what they were before, but remain loyal to the elder brain and seek to return to the fold as it's their natural state of being. Mind flayers whose elder brains died, or who were excluded may have resisted attempts to bring them under the control of a foster brain, but those created by an elder brain would usually seek to return to it. The Emperor clearly states that he was changed at Moonrise Towers. While the Emperor had been free for some time, Gortash probably only saw a powerful champion for his cause and didn't expect the mind flayer to have second thoughts about it and not be 100% loyal to the grand design. In Act 3, the Emperor had to specifically extend "his" protection to Minsc, so at that time the prism did not work with a simple area effect. Maybe it did do that while it was still in Githyanki possession, but we can't tell.
Mephistopheles is stated as being Raphael's father on bg3.wiki. Therefore, Rafael's plans of ruling the hells and beyond may simply be those of his daddy who hated ruling only over the desolate cold of Cania.
