I've always wondered this as well. At what point does Panam notice it's Johnny not V. Did she try and confront Johnny at camp and he ran away, or did he sneak away as soon as he'd recovered. Did Johnny pretend to be V long enough so that he could leave, or did Panam cotton on straight away that it was him?Yes this was a missed opportunity. Though I assume V would have been unconscious for most of the escape from Arasaka tower.
Also this reminds me of a plot hole. When V gives Johnny the body wouldn't Panam have recognized this as they were riding back to camp? It might be a good question to ask Pawel.
Quite the plot hole...