Remember.. there was a pecking order on the star trek series as well. It makes perfect sense that you do not have 5 commander level assignment consoles at 5. That you have, just one. And then a Lt. commander, two Lt's, and a ensign.
On the very rare BO's, there are certain bo skills that you can "only" get from the very rare ones, such as the Commander ability, Reverse Shield Polarity III. You cant earn the right to train it as the captain from skills, the npc's at spacedock cant train it, and so far nothing under Very Rare BO quality has had it. Even then, it is rare to even see it on the Very rare quality ones.
You can thus trade for what you want, for your ship. Not everyone has RSP III that is an engineer captain.
Using the example of reverse shield polarity III, though, I'd have to be on a cruiser to even be able to use it.
So what is all the hoopla? Just the character traits? I wish we could use all 4 space abilities just like ground ones.
Using the example I used, no matter what ship you pick, you will be have the oppurtunity to use a ability you can only get from the very rare bo's. There is more than one. I know Engineering, I've only Seen RSP III and Emergency power to Structual Integrity Field III on the very rare BOs. Be different abilities, but some for escorts and science ships.
If you could use all four, then there would be no choice needed, and with no choice, you might as well have it all from the getgo.
I am unsure if your just trying to push a arguement as of right now. You will, regardless of ship, and if you utilize a very rare BO with a rare III ability, have something you otherwise couldnt. It does not matter on your captain class, your skill selections.
All that matters.. is what ship and the chance at the BO ability. It is a small boon, a lucky roll. A bonus good skill, most times, that you can aim to obtain.
the entire Rank/level thing is funky, let's be serious now does it make any sense to have a Admerial with a single ship that is full of Captains for every BO?
I'm honestly not sure exactly how the bridge crew complement breaks down by rank (in canon), but considering the game lets you HAVE 4 officers on your bridge crew that are Commander level, you should be able to use all their skills up to their max rank.