It's natural for people (including NTs) to experience a brief episode of the fight or flight response when suddenly woken from deep to moderate deep sleep, even if it's at a routine time. Your response is due primarily to what stage of sleep you're in when you awake, and if your fight or flight response is triggered (like being touched abruptly or by an alarm going off), you will naturally react with irritability or a slight surge of adrenaline. This is nothing out of the ordinary. If this happens to you regularly then:
1) You are probably not getting as much sleep as you individually need (which can vary from 6 to 10 hours, on average), so you end up having to wake up or be woken up during your deeper sleep cycle
2) Your sleep patterns are probably too erratic and so your natural cycle of falling asleep/light sleep/deep sleep/light sleep/waking up is out of whack
3) Although the first two are MOST likely to be the case, in a few cases, people with pre-existing anxiety disorders may have a problem with sleep in general (and this can be often be treated effectively with SSRIs, provided, of course, they are sleep enough and at a regular time)
Most people, even those with ASDs, should be able to sleep and awake normally if they get enough sleep and stick to a routine sleep schedule. Sleep is hugely important to your health, espeically your neurological and psychological health. Yet most people treat it like it's some sort of inconvenient distruption of one's life and so they failt to give it the prioroity it deserves. So of course, this behavior will inevitably lead to problems, like feeling stress and anxiety when you have to wake up. However, this simple logic is largely lost on the modern masses today, including many ASD people. Go figure.