Wow, I can't believe you put sensors in the bed, that is awesome. You are completely correct though, an alarm clock should be next to the bed not in it.
But you don't need to know what cycle your customer is in to implement a gradual wake up process. You can just assume they are in the deepest sleep, start incrementing, and eventually the alarm clock will be in sync with their current state of sleep.
Again, the product looks great.