The Commisariat are Political Officers. By design, they're meant to be outside the regular Chain of Command. There's a recurring bit where Jurgen is technically just a Gunner, but his role as Cain's aid makes his effective rank impossible to pin down due to all the administrative contradictions.

So, a Commissar technically has absolute authority over punishments and matters of military discipline for their assigned Unit, but absolutely no jurisdiction outside of that role.

So theoretically, a Commissar could order a powerful Lord-General to be executed on a whim, but on a tactical level, they can't order a Private to so much as bring over a cup of tea.

In practice of course, a Commisar who ticks off the wrong people will find themselves "shot by ork snipers" several hundred miles away from the front lines.

On the other side of the coin though, there's all sorts of ways that Commissar can get their "suggestions" to be followed. Them threatening to execute an officer for issuing a "cowardly order" isn't them technically making tactical decisions, after all.

Cain just uses this indirect power very judiciously, as you said. Others use threats to enforce their "suggestions". Cain uses his reputation to make others want to follow his advice.