you have a choice locked by being the most-skilled pilot and choosing it leads to one set of the best ship parts. How does that flow?

You got my idea wrong

you get access to better parts by completing faction missions,

I meant that, as a reward for finishing a quest, or series of quests, the ship parts become available. It's not "choose to get a ship part during the quest", it's "complete quest, vendors now sell new stuff".

For instance, completing mission 4 of the UC Vanguard opens up B class parts because "congratulations, we're promoting you" or, given how that questline flows, "We're promoting you because things are getting dangerous and you need access to the extra stuff". Completing the final mission unlocks C class parts. But those are only at the Deimos Staryards, since they're the sole contractor for UC. It wouldn't make sense to complete their questline and also get access to FC's B and C class ship parts, for that you'd have to complete their Freestar Ranger questline. That's the idea.