en.m.wikipedia.org
I couldn't find any useful proof links in that article. It is unclear why the described behavior was presumed to be instinctive. Just because some scientists may think it's instinctive doesn't necessarily mean it's true.
It's rather difficult to distinguish whether a behavioral pattern is "programmed" as a whole or is composed from more primitive skills, some of which can be innate and some of which can be learned.
That said I do dispute your definition of "instinct". It doesn't have to be conscious. Jumping at a loud noise is not conscious but is instinctive.
I think, you confuse instincts and reflexes here. Although the difference between the two may be subtle, unconscious responses are typically termed "reflexes" rather than "instincts".
Our ancestors have had to deal with drowning for much longer than they have had to deal with standing on two legs, and as long as we have had to deal with suffocation or loud noises. It's an experience which is strongly associated with death, and we can therefore expect selection to occur. It should not be surprising that we have instincts relating to it.
Such considerations may be sufficient for making hypotheses about instinctive nature of responses to drowning, but they don't actually prove that your brain would instinctively try to save you despite your will.
The initial discomfort associated with water boarding is not primarily asphyxiation, it is having water run up your nose and begin to flood your airway. People can hold their breath for at least several seconds to avoid asphyxiation, but that doesn't work for waterboarding, where the panic sets in almost immediately when water flows up the nose.
That's actually easy to reproduce and check. It doesn't work on me like that, so I conclude it's just a myth.
I can also speak from personal experience of trying to drown myself in the bath, which is obviously different because it's so easy to abort - strong panic response.
I had an opposite experience. I tried to hold my breath underwater as long as possible many times and I used hyperventilation to delay the urge to breathe. Once I was curious whether I can bear that urge which eventually appeared every time and I was able to resist against it using my will power. After nearly a half-minute, strong desire to breathe became not so strong and a few seconds later I became completely calm. I started to think about unrelated things and almost lost my sense of where I was.
Luckily, SWB didn't come instantly, I was able to notice that I was about to losing consciousness, so I quickly left water and started to hyperventilate, since I didn't plan to CTB at that moment. If I intended to die back then, it would be rather easy to do - I should have waited just a few more seconds to reach a complete blackout.
I had no any feeling of fear or panic when I was underwater, some fear appeared only when I resumed breathing and realized how close I was to death and thought about possible aftereffects, since I had unusual numbness in the head and the whole body that I never felt before that dangerous experiment.