I would make them the same size. This isn't so much because of the piping but because of the 'turn of the cloth' effect.
When you're making a collar from a thicker fabric, the upper collar needs a little extra to wrap over the undercollar. As the PJs will be in a finer fabric (this counts for blouses, too) there isn't so much bulk for the top collar and lapels to wrap around, so you shouldn't need to worry about the turn of the cloth effect in this instance.