You don't mention, or I missed, how old your son is. Worktime in a Montessori school is all the time. The things the children do are referred to as work, so there's not playtime/worktime. Some kids prefer different activities in Montessori classrooms, and it's the teacher's job to make sure the kid is getting a varied "diet", not just doing the things he or she wants to do all of the time. It's great that he's getting better at choosing his own work. It takes a while for the student to "normalize" into the routine AND for the class itself to normalize.
I'm not a potty expert, but maybe he's not completely ready for autonomy in this area. My own son took FOREVER to be ready to potty completely on his own. The Montessori preschools I know will expect the child to be independent in this area. Someone should have shown him, early on, the toileting routine, so he should know that going potty doesn't indicate he wants to rest. Maybe that wasn't made clear to him.