Am I correct in that the V+おう form could formerly be used in place of Vだろう?
Yes, in the sense that it could be used both formerly and also contemporarily.
I've heard a phrase「控え居ろう」, which means "get on your knees", if I remember correctly.
I believe that your remembrance of this phrase’s meaning in its context (水戸黄門？）is clouding the actual meaning. In this usage, おろう serves as an imperative, and would probably use an exclamation point. This would mean ‘Restrain yourself!’ and would be interpreted as ‘Show the proper respect!’ to indicate that the other party is being impertinent. It can be paraphrased as 'Shut up and wait'. It is equivalent to hearing「控えなさい!」whereupon, the receiver of this rebuke is forced to show contrition by kowtowing.
What is the meaning of the presumptive form here?
In the modern language, you can use -おう only to suggest first-person actions.
I don't follow... It is often used when giving instructions or admonition to a second party, 「ゴミはゴミ箱に入れるだろう。」’We put our trash in the trash can, don’t we?’ or 「もっと早くやりましょう。」'Do it faster.'.
Is おろう a presumptive form for both いる and おる?
It can be used for either. いる and おる are just different pronunciations of the same word.
おる was once the more common way of pronouncing 居る and it has retained dominance in certain parts of the country (近畿、中国、四国）and especially among some older denizens. In some areas, it is even considered honorific language.