My sister-in-law fought the designated binder and planner issue in middle school. Ultimately, she won them over by proposing a one week trial using her daughter's preferred system. Her DD showed significant improvement during that week and was allowed to keep using her system.

Another thought, any chance that he could turn in assignments electronically, i.e. scan and email to teacher, thus eliminating the paper issue?

Good luck fighting the well-intentioned, but flawed, system.