I think what you are calling the plunger rod is better described as the pushrod, the plunger being the part up inside the cylinder bore with the two seal caps and the spring. The plunger and pushrod form a ball and socket type joint with the plunger being the socket and pushrod the ball. The seal is above the socket on the plunger so this joint itself has no sealing function. There is no physical connection, they just fit together and it allows a small amount of pivoting movement. There should also be a large flat washer and c-clip on the pushrod to hold it all in place. This picture shows the parts in order with the boot removed for clarity.