Your entire gender bias was based on anecdotal evidence. This example of yours is not used to calling other people Sir. As an army brigadier he received more "Yes Sir" than he gave. If he chose to be subservient it would more likely be a personal trait. In fact, the stereotype of such a high ranking officer is one of arrogance rather than subservience.
At his level, when he uttered a "Yes Sir" it would have to be for a formal event like a parade drill or responding to an Operation Order to show that it was being understood. In a military environment, there is no room for "if" or "but" or "maybe" because the clock starts ticking the moment the Operation commences. You have to understand that this has nothing to do with being subservient.
An army brigadier after so many years in such an environment respecting the orders of a superior may developed a respect for higher authority. Even that this applies mainly to formal orders. For a commander that is worth his salt, he should have his own ideas to contribute. Otherwise he would not have risen that far.
NSmen, on the other hand, don't have that many years to develop any special respect for authority. If you have the opportunity to manage NSmen, you would know that it is not easy to get NSmen to do things, you need to persuade, to reason, even to urge.