That certainly seems like a fair interpretation of the situation, but what about the following. The crew of the rogue trader know about the dark eldar and are a pretty dodgy bunch. The dark eldar, when not fighting for the rogue trader (and his own pleasure) engages in pit fights on the lower decks. The combatants win a months paid shore leave (or freedom depending on the type of ship) if they can hit the dark eldar. The dark eldar does a lot of show boating (takedowns) as well as being able to fight a range of combatants. This again would allow the dark eldar to amass a lot of pain tokens during the course of a voyage or even a few hours before making planetfall.
It would, and the Dark Eldar are well-inclined towards gladiatorial combat, but those terms seem frankly tame - an attempt more to 'game the system' than playing to type. Further, if the crew figure out that he's only fighting to stun, they're hardly going to fear him… and fear and pain are literally the food and drink of the Dark Eldar.
Are there any guidelines on what this rate should be? When you say rules are designed to allow for out-of-combat torture, does that mean that the other sources of pain tokens (stunning, pinning checks, fear, e.t.c) only apply in combat and not narrative time (with the 1 Pain Token per X amount of time taking precedent in narrative time)?
I would say so, yes, particularly if you're trying to deal with a protracted period of time. Pain Tokens are session-by-session, exchanged automatically for Fate Points when you accumulate the right amount (which increases as you gain Corruption - a particular worry if you habitually use combat drugs), and those Fate Points vanish at the end of the session if not used. In essence, they're not a resource that can be endlessly stockpiled. Further, the talents that key off Pain Tokens work only when gaining Pain Tokens during that encounter - stockpiling beforehand doesn't help use those abilities.
Broadly speaking, a Dark Eldar character should have opportunities to accumulate Pain sufficient to give him two to four Fate Points a session if you want parity with the rest of the group). That's typically 20-30 Pain Tokens, though some of that can easily come from simply hanging around the rest of the party during combat and feeding off of the consequences of their mishaps, and it's not too hard to pick up several in a short space of time with the right tools and talents. For any given bout of torture, I'd use the Interrogation, Medicae or Intimidate Skills to moderate the amount - a Test takes an hour (less 10 minutes per Degree of Success) and yields a Pain Token if successful. The "Artful Torment" option in the Xenos Origins: Vile Pleasures section doubles this for would-be torturers.
As a rule of thumb I'd say that any given Pain Token, if unspent, fades after 24 hours (looking back on my original notes, that was originally the case, but there were a few details that got shoved out of the manuscript over successive drafts as I tried to turn a concept that was simple in my head to one that was clearly explained on the page… not always an easy task). That serves well to prevent stockpiling Pain Tokens over long voyages, while still encouraging those sorts of activities as a means to keep the Dark Eldar 'fed' (though 'feeding' off the crew reduces Morale).