I would keep him separated at least until all of his adult feathers are in and maybe even until he is needed in the breeding pen. For me my responses to him are not to his aggression or submission. To start things off in a new direction, pull him off roost for move to his private quarters. Avoid stressing him during day as he will enter that into his calculations as to whether you are a threat he can beat. I like so they do not think I am a threat at all. A cockerel showing aggression towards birds outside his "subflock" / family group is generally not a concern. I see that every day and do not associate that with problems later with my birds and how I interact with them.