There's also the scene with old Aeryn and Pilot before she leaves Moya, which shows that at this stage the show remembers their relationship despite being mostly a John/Aeryn ep.

Don't know if you noticed, but old John's Southern accent is significantly stronger than most of the time in the show.

Also, before the reverse Starburst, Pilot yells "Kahaynu preserve us", which definitely shows how much he bought into the events of "Look at the Princess" being necessary.

And a plot hole that has always annoyed me in this episode - since she'd been living all that time on the planet and not been trapped in the pod, why was the pod completely overgrown with Zhaan's herbs when Aeryn got back?