Joint legal custidy and primary physical custiday/ Does this give the parent the right to choose schools if other party has primary decision making for schools?

First, it's custody.

I don't know what you are asking. One parent has physical (custodial) custody of the child but the non-custodial parent makes the school decisions?

What does the Court Order say?

If they have joint custody ( each person getting child 1/2 of the time) such as every other week. Often it will be spelled out specificly what school district the child has to stay in.
But even with joint custody, each in Georgia should be spelled out in the custody, who has control over schools, over medical and over 100 listed items. Now often on schools and non emergancy medical, some require both parents to agree before schools can be changed.

The custody agreement if properly done spells this all out, if not and there are issues, you end up back in court to work them out.

But if the child custody agreement gives one parent the right to make choices in education, the other parent will not have that right, even with joint custody