I'm not a mod, of course. But I'm always up for research.
So lessee. For the superior soldiers, seems that after about a month in, you get that rank. Midshipman is an entry-level rank, but Shoi is not. However, you could get bumped to it in the same amount of time. The commanders determine this, of course. So superior soldier's a rank you earn, to some extent.
Now for the warrant officers. By crew roster, we have one warrant officer per ship. That alone says the position isn't easy to obtain, so it might deserve some extra money. Along with that, midshipmen are cadets. Would you still pay them more than a warrant officer that's been in the service for a while? Me, I dunno, but that's an argument.
The Sakura's WO was appointed to said position.
The Celia's was promoted from Nitô Heishô, but she's a medical officer (and discharged).
Another former WO was an NPC and got axed anyway.
The 5th's doesn't have a promotion logged, but the bio says he started as rank "Juni." He's still about, but in what capacity, I don't know. His board rank is Taii, so I'm wondering where the promotion is.
Last, the Mikomi's in 4th fleet, and doesn't have WOs directly. Regardless, the Mikomi has none.
Again, I'm taking this as Juni is a harder rank to get, and is awarded to those who ask for it (but have the time put in). The Juni on the Sakura, for instance, is a bodyguard for a Taisa. That's something.
So, maybe that justifies the pay scale some? But I do agree, entry-level soldiers should get paid something. I guess the starting bonus is what that is.