Hi - welcome to the forum, and glad you've been enjoying the game!
It's close what what SCC said, yeah - the "elite" skill levels are mainly there to give the player a "special" bonus for picking something that only affects their piloted ship, so that you can feel like you're getting something you wouldn't get just from a high-level officer, and so that you can feel that - even with relatively few combat points spent - that your character is a capable pilot; in some ways more capable than the officers under your command. And by requiring story points to unlock these - instead of making them just player-only portions of skill effects - it makes this feel more earned.
This really applies even if you're using autopilot, though you'd naturally get more value out of it depending on how much personal piloting you do and how well you do it.
Non-combat skills don't face the same situation where lots of NPCs visibly have them, and you're comparing your character against them - I mean, admins have some of them, and fleet commanders have some some of the fleetwide skills, but it's much more minor - so there's not much point to locking some of the effects behind a story point. Basically, it's less a progression system for skills and more a way of gating access to some of the effects, and this, imo, only really makes sense for combat skills.
Plus, for combat skills, the "elite" effects are usually something cool and particularly powerful, which is easier to get away with because it's still just one ship. For fleetwide/colony skills, the effects would have to be much more restrained, so it wouldn't be as exciting and would probably just feel like a story point "tax" to unlock the full value of the skills.