Oh yeah, Proton saw him. He regarded Cyrus somewhat apprehensively, watching him closely as he wandered. Not only did he look like a weirdo, but Proton was still wary about letting people know straight up that he had Pokemon, though he had mentioned it in passing several times already. He did happen to have some of the iconic Team Rocket Pokemon, after all, and he didn't want them to be a dead giveaway.

He made sure he knew where each one was as Cyrus got closer around the lake. And, of course, instead of ignoring the guy like a smart person would, Proton basically challenged Cyrus with his eyes to bother him, when he was within eyeshot.