Agreed, it is what you are used to. There was a combination of mainstream music (4/4) and classical growing up, so I don't find other time signatures a problem, in fact for listening music I prefer them, but there are some genres that it doesn't work, and some people that just haven't been exposed to anything else who can't cope.
But we don't have one natural scale, we have several depending on the instrument. The scale on a piano is different from the scale on a guitar, even if only slightly.
If someone has perfect pitch (compared with someone who just says they have which is a much larger segment), they can literally hear the frequency, which means if it is somewhere between an F and an F#, they will know that, because they can hear the pitch. I have only met 2 people with perfect pitch, but a lot more than claim to have it.
And.. we are all born with the ability to have perfect pitch, but most of us lose it due to a lack of exersize.