If that's a Schrader valve (tire valve) it's used to test the low pressure or suction side of the system or add freon.
After all these years there's a good chance your coil or the one you're replacing has been changed before and either, or both, are aftermarket and might be slightly different to include the valve or not.
Usually the high and low pressure connectors are on the engine side of the firewall. I don't know anything about AC on the YJ or where the valves are located on the original equipment.