The Hidden Memory (2) - S1-E20
Visible crew/equipment: After Pilot (on viewer) tells Rygel and Chiana, "Moya's data stores indicate it may be best to get the offspring out as fast as possible," when it cuts to Rygel's close-ups we can see the blonde head of the puppeteer at the lower left side of the screen.
The Hidden Memory (2) - S1-E20
Visible crew/equipment: After the shot of Gilina, Aeryn, and John crouching under a floor grate, while hiding from the PKs, it cuts back to Moya, and just as Chiana reaches Rygel we can see the base of his hoverchair.
Chosen answer: It's never explained. John mentions a theory that his less technologically developed craft simply interferes with the wormhole less than the "superior" Vipers, but they never make a concrete determination on that point. But we also have to take into account the fact that Moya traverses wormholes with no ill effect as well.
Garlonuss ★