Political scientists often differentiate between "authority" and "influence" within any political setting. Authority
is generally derived from the official positions of state, usually in some form of formal hierarchy. Influence
is an abstract measurement of other means of power - personal affiliations, private wealth, or, in the case of the Sith Empire, strength in the Force. In any system of government, an individual's influence may be very different than their titular authority.
In general, authoritarian governments often have (perhaps ironically) very unclear structures of authority, often with entirely parallel systems of government existing simultaneously. Competing lines of authority actually help to secure the power of the national leadership, since competing bureaucracies are unable to adjudicate disputes amongst themselves, and must continuously turn to the national leader to make decisions. One might expect that the Sith Empire, with its 12 quasi-independent Spheres
, is designed to operate along these lines, securing the Emperor's place as the ultimate arbiter.
On the question of Sith philosophy, it actually makes a lot of sense that Sith government would be organized along lines of influence rather than along lines of formal authority, since Sith believe that the powerful should rule and the weak should perish. Formal authority rests on a series of rules and customs that (in the Sith opinion) serve to restrain the truly strong from seizing power. In a system of pure influence, however, those with the greatest influence rule the society, regardless of titular positions of authority. Thus it's not surprising that an influential individual like Kilran or Malgus would behave peremptorily towards others, even if his actual position of authority were not particularly strong.