Without examining what Kup had become, there's no way to know how much left was Kup, and how much was Prowl. Perceptor knows what his alterations should have allowed Prowl to do... but he can never know how much Prowl corrupted those changes to give him more access. Perceptor had learned to expect the worst.

And, maybe, there was just a part of him that hoped that it hadnt been Kup who'd left him behind on Turmoil's ship, but that it had been Prowl

"I could have refused. I should have refused."