I had a thought about these.
Dark Blood units in particular, seem odd.
the regular covenant forces include battleships and the like, so it's not military objectives that the Dark Blood people would be concerned with.
So, it would be more... political ?
In the few missions where you see a Dark Blood commander, such as COSMOS missions, they're participating in quite politically important things. Not simple slave raids or anti-shipping campaigns, but things of a more theological or political importance.
So, I'm thinking that the commander ships, represent something where there is a relatively important objective that is not necessarily military in nature.
Like having some attached officers from the Intelligence services along on a military expedition.
Might go for the other types of commanders too.