Good companions can teach you their skills with good relations: Borcha (with tracking), Rolf, Melva, Oguma, Secret Man.
If you choose a companion as "commander" in "troop setting", you get to play as that companion. So, you can play as Jormie if you like.
And yes, it's for balance issues. There's a reason there's only 3 dark commanders.
Also, because you can get the "sunflower scroll" instead of the secret scroll, it would be not make sense to be able to simply learn any equivalent special skill from a NPC.
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mainly for Nora Lee
Balance Issue:
I am of the opinion, that the 3 dark generals are not balanced however, as I believe Jormungand (with leadership14 !?) is so much more powerful than Fenrir or Hel.
I believe Fenrir needs to be stronger, as he is a dark knight, but has a little low power strike (compared to Jormie). Fenrir needs a stat boost, especially since his special skill is not as powerful as Hel's or Jormie's, and the AI cannot make proper use of it too.
I also believe Hel can use a bonus to power draw, or simply better skills overall, since she has low power strike, low HP AND not so great armor (although she's sexy!). Hel is better than Fenrir however.