Lets focus on the first quetion.
Ingrained are those ideals on which professional conduct(and not just the art of war) is built on..or inculcated if one is to use it. It does not have to form part of a curriculum, rather the organizations culture.
Does the culture teach when to say "yessir" and salute , whom to talk lightly to and whom to give a piercing look? Perhaps and perhaps not.. since these values are carried forward by what one brings to an organization.
But does culture affect how one looks at certain issues and the bias one takes into analysis?
Its quite possible..
Does the culture extrude a constant threat perception of India(or used to)? Does that extrude a sense of Muslim military superiority under all conditions(Or did)? Did that factor into the military strategies that led to our downfall at many instances?
Let me respond to you for what I understood from your post. Like I said earlier, I am not a soldier by profession and whatever I state here is because of my interaction with some friends and my personal interest in matters related to geo-strategy and military. I may be wrong in certain things and may be forgiven for inaccuracies.
After the officer passes out from military academy, he joins different arms like infantry, armoured tanks, artillery and various supporting or logistical echelons. The grooming of the officer is undertaken by the particular unit or entity that he or she joins. Interestingly, the culture of grooming and training differs in different arms or logistical and supporting echelons. I found that those arms who fight upfront, like armoured tank or mechanized infantry or infantry without carriers, a lieutenant is called a Mister in many units. In some places I saw these young ones initially living with their soldiers for a considerable period of time. They are made to do all what the soldier is supposed to do and after a prescribed time, they take over their duties as officers commanding small echeloned sub units. Their initial life is pretty tough. They are taught etiquettes and mannerism in the unit messes and by the senior officers. They learn professional know how from soldiers as well and professional ethics from their senior officers.
Initially, they just listen and observe and are taught and I didn’t see many even open their mouths infront of their senior officers. As they grow in rank and service, many go out for different courses to military institutions for specializations etc. When they come back from these, and grow in stature a bit, they do ask questions and at times embarrassingly blunt ones. There are some very good senior officers and some very strict ones as well. Their professional grooming is almost identical with what takes place in many other modern armies.
The logistical and support echelon people have a bit different style of grooming. These are not as strict as the ones that I talked about. And probably rightly so because their line of work is totally different. Howeve, when they would go out in the field, all would function professionally. Out in the field, there are heated professional discussions about whatever they would discuss and young and old are encouraged to participate. There is no discriminatory aspect where a junior officer may not be allowed to but in and speak. They are respectful yet very aggressive at times while putting across their viewpoint. Once they decide upon what to do and how to do it, all go around their business professionally.
While visiting friends, there were certain units where I saw mosques inside the units probably because there was no other mosque located nearby. The presence in mosque was probably not mandatory. Because I went for Juma prayers once and not all the guys were present there. Many just went about their work while the prayers were on.
Our threat perception is more or less India centric. And this reflects on ground as well. And this even I understand well because around 80% of Indian Army is deployed against Pakistan. And if one does not become India centric when such a large number threatens you from their deployment pattern across the border, it would certainly be foolhardy.
During my interaction with my military friends etc, I never even once found them discussing their being Muslim as a superiority thing for them. They would discuss Indian weapon systems, Indian tactics, their deployment pattern etc etc but never heard them saying that 1 Muslim = 10 Hindus as some of the Indian gentlemen here are so vociferous about.
You forgot history 
